user16806: Over a period of last few years I have almost completely eradicated the 'five hindrances' to meditation. However, sometimes when I am in deep meditation, I feel an intense fear of 'getting annihilated' and then my mind immediately becomes restless and meditation is broken. As the mind knows that total emptiness will be the end of 'mind' or 'ego' I think the fear springs from that idea.
How can I overcome this fear when the meditation is going on? and also, I wonder why 'fear' is not listed as one of the five hindrances to meditation?

user21750: "As the mind knows that total emptiness will be the end of 'mind' or 'ego' I think the fear springs from that idea."
Then simply let go of such ideas and ways of thinking about being or not-being (as both is wrong thinging). Just 'this isn't real, lasting, worthy to hold on it, make it mine.' The hindrance is simply doubt, and possible caused by neither listen to the good teaching or with wrong attention (e.g. lack of good association). What should be feared to get lost if of no worth and the Buddha didn't thought of others to just get lost. Does this arising thought, idea last? Real? Then, go on for heartwood beyond it, just knowing 'oh, this thought'.

user471: The Visuddhimagga or the Path of Purification by Ven. Buddhaghosa is useful for this purpose. Please see "Path of Purification (Visuddhimagga)", translated from Pali by Ven. Ñāṇamoli. It's a classic manual of Buddhist doctrine and meditation written in approximately the 5th century CE, and is considered the most important Theravada text outside the Pali Canon and its traditional commentaries.
It talks about the eight knowledges of insight:

Now,  insight  reaches  its  culmination  with  the  eight
knowledges,  and knowledge in conformity with truth is ninth; these
are what is called purification by  knowledge  and  vision  of  the
way.The  eight  should  be  understood  as  follows:  (1)  knowledge
of  contemplation of rise and fall, which is insight free from
imperfections and steady on its course,(2) knowledge of contemplation
of dissolution, (3) knowledge of appearance as terror, (4) knowledge
of contemplation of danger, (5) knowledge of contemplation of
dispassion,  (6)  knowledge  of  desire  for  deliverance,  (7)
knowledge  of contemplation of reflection, and (8) knowledge of
equanimity about formations.
“Knowledge  in  conformity  with  truth
as  ninth”  is  a  term  for  conformity.So one who wants to perfect
this should make these kinds of knowledge his task, starting with
knowledge of rise and fall free from imperfections.

The description of (3) knowledge of appearance as terror:

As  he  repeats,  develops  and  cultivates  in  this  way  the
contemplation  of dissolution,  the  object  of  which  is  cessation
consisting  in  the  destruction,  fall and breakup of all formations,
then formations classed according to all kinds of becoming,
generation, destiny, station, or abode of beings, appear to him in the
form of a great terror, as lions, tigers, leopards, bears, hyenas,
spirits, ogres, fierce bulls,  savage  dogs,  rut-maddened  wild
elephants,  hideous  venomous  serpents,thunderbolts,  charnel
grounds,  battlefields,  flaming  coal  pits,  etc.,  appear  to  a
timid man who wants to live in peace. When he sees how past formations
have ceased,  present  ones  are  ceasing,  and  those  to  be
generated  in  the  future  will cease  in  just  the  same  way,
then  what  is  called  knowledge  of  appearance  as terror  arises
in  him  at  that  stage. ...
But  does  the  knowledge  of  appearance  as  terror  [itself]  fear
or  does  it  not fear? It does not fear. For it is simply the mere
judgment that past formations have ceased, present ones are ceasing,
and future ones will cease. Just as a man with eyes  looking  at
three  charcoal  pits  at  a  city  gate  is  not  himself  afraid,
since  he only  forms  the  mere  judgment  that  all  who  fall  into
them  will  suffer  no  little pain;—or  just  as  when  a  man  with
eyes  looks  at  three  spikes  set  in  a  row,  an acacia  spike,
an  iron  spike,  and  a  gold  spike,  he  is  not  himself  afraid,
since  he only  forms  the  mere  judgment  that  all  who  fall  on
these  spikes  will  suffer  no little pain;—so too the knowledge of
appearance as terror does not itself fear; it only forms the mere
judgment that in the three kinds of becoming, which resemble the three
charcoal pits and the three spikes, past formations have ceased,
present ones  are  ceasing,  and  future  ones  will  cease.

The description of (4) knowledge of contemplation of danger:

As  he  repeats,  develops  and  cultivates  the  knowledge  of
appearance  as terror he finds no asylum, no shelter, no place to go
to, no refuge in any kind of becoming,  generation,  destiny,
station,  or  abode.  In  all  the  kinds  of  becoming,generation,
destiny, station, and abode there is not a single formation that he
can place his hopes in or hold on to. The three kinds of becoming
appear like charcoal pits  full  of  glowing  coals,  the  four
primary  elements  like  hideous  venomous snakes (S IV 174), the five
aggregates like murderers with raised weapons (S IV174),  the  six
internal  bases  like  an  empty  village,  the  six  external  bases
like village-raiding  robbers  (S  IV  174–75),  the  seven  stations
of  consciousness  and the  nine  abodes  of  beings  as  though
burning,  blazing  and  glowing  with  the eleven  fires  (see  S  IV
19),  and  all  formations  appear  as  a  huge  mass  of  dangers
destitute of satisfaction or substance, like a tumour, a disease, a
dart, a calamity,an affliction (see M I 436). How?
They  appear  as  a  forest  thicket  of  seemingly  pleasant  aspect
but  infested with wild beasts, a cave full of tigers, water haunted
by monsters and ogres, an enemy  with  raised  sword,  poisoned  food,
a  road  beset  by  robbers,  a  burning coal, a battlefield between
contending armies appear to a timid man who wants to  live  in  peace.
And  just  as  that  man  is  frightened  and  horrified  and  his
hair stands  up  when  he  comes  upon  a  thicket  infested  by  wild
beasts,  etc.,  and  he sees  it  as  nothing  but  danger,  so  too
when  all  formations  have  appeared  as  a terror by contemplation
of dissolution, this meditator sees them as utterly destitute of  any
core  or  any  satisfaction  and  as  nothing  but  danger.

Apparently, this will transition into a knowledge of peace:

“He  contemplates as suffering
Arising, occurrence, and the sign,
Accumulation, rebirth-linking —
And this his knowledge is of danger.
“He contemplates as bliss no arising,
And no occurrence, and no sign,
No accumulation, no rebirth-linking —
And this his knowledge is of peace.
“This knowledge about danger has
Five sources for its origin;
Knowledge of peace has also five —
Ten knowledges he understands.


Knowledge of the state of peace is this: “Non-arising is safety,”
etc.: this, however, should  be understood as said for the purpose of
showing the opposite kind of knowledge to knowledge of danger. Or when
it is stated in this way, that there is safety without terror and
free from danger, it is for the purpose of comforting those  who are
upset in their hearts by seeing danger through appearance as terror.
Or  else,  when  arising,  etc., have clearly appeared to a man as
terror, his mind  inclines towards their opposites, and  so this is
said  for the purpose of showing  the advantages in the knowledge of
danger established by the appearance as terror.

So, the mind first sees the terror of the inevitability of the cessation of phenomena, and then experiences danger when it realizes that there is no place to cling to for safety from the inevitability of the cessation of phenomena. Finally, it accepts this situation, and sees non-arising etc. as safety.
Is fear not one of the five hindrances?
Well, if the terror of the inevitability of the cessation of phenomena, or the danger of no place to cling to for safety from cessation, hinders one from progress due to fear, then this falls under the hindrance of doubt or uncertainty (vicikicchā), in my opinion, because the mind is doubtful and lacks conviction and trust, on whether it is the right way forward.
The same text states:

It is without wish to cure (vigatá cikicchá), thus it is uncertainty
(vicikicchá). It  has  the  characteristic  of  doubt.  Its
function  is  to  waver.  It  is  manifested as indecisiveness, or it
is manifested as taking various sides. Its proximate cause is unwise
attention. It should be regarded as obstructive of theory (see
XVII.52).


user13992: In a way, fear of annihilation is part of the five hindrances, for example:

attachment to/desire for the continuation of sensory perception (i.e. to the physical body)
resentment/bitterness toward mortality
doubt in the concept of Anattā

Since individualism is a central tenet of Western civilization, it can be especially hard to anticipate 2 annihilations: the inevitable death of the body and the annihilation of self (the latter in Zen is called "the Great Death") as a necessary step in attainment.
In addition, in Western culture we tend to "hide" death as much as possible, compared to Asian cultures. For example, there is a long tradition of monks meditating around a deceased person in Asia - not to mention the tradition of Tibetan sky burials. You might say we "push death away" much more in Western culture.
As a consequence, we perhaps tend to "push Anattā away" in the same way we avoid being confronted with physical death (consciously or culturally). I struggled with this my "self", until my teacher urged me to really mentally dive into what really discomforted me regarding this idea - and that's all it turned out to be in my case: the imaginings of what the actual event of self-annihilation would be like. Like what most people fear about physical death is not death itself, but the way it will come, I had formed the most terrifying scenarios in my head what this "dying process of the self" would be like. I would almost call it "spiritual hypochondria" in my case.
Needless to say, all these imagined scenarios were completely absent from the initial glimpse of the actual experience (in my case through Kōan practice). But I did need that initial push from my teacher to dive into my extreme discomfort of the idea to get there.
Hope this helps.

16806: <p>Over a period of last few years I have <em><strong>almost</strong></em> completely eradicated the '<a href="https://en.wikipedia.org/wiki/Five_hindrances" rel="nofollow noreferrer">five hindrances</a>' to meditation. However, sometimes when I am in deep meditation, I feel an intense fear of '<strong>getting annihilated</strong>' and then my mind immediately becomes restless and meditation is broken. As the mind knows that total emptiness will be the end of 'mind' or 'ego' I think the fear springs from that idea.</p>
<p>How can I overcome this fear when the meditation is going on? and also, I wonder why 'fear' is not listed as one of the <a href="https://en.wikipedia.org/wiki/Five_hindrances" rel="nofollow noreferrer">five hindrances</a> to meditation?</p>
 21750: <p>&quot;As the mind knows that total emptiness will be the end of 'mind' or 'ego' I think the fear springs from that idea.&quot;
Then simply let go of such ideas and ways of thinking about being or not-being (as both is wrong thinging). Just 'this isn't real, lasting, worthy to hold on it, make it mine.' The hindrance is simply doubt, and possible caused by neither listen to the good teaching or with wrong attention (e.g. lack of good association). What should be feared to get lost if of no worth and the Buddha didn't thought of others to just get lost. Does this arising thought, idea last? Real? Then, go on for heartwood beyond it, just knowing 'oh, this thought'.</p>
 471: <p>The <a href="https://en.wikipedia.org/wiki/Visuddhimagga" rel="nofollow noreferrer">Visuddhimagga</a> or the Path of Purification by Ven. <a href="https://en.wikipedia.org/wiki/Buddhaghosa" rel="nofollow noreferrer">Buddhaghosa</a> is useful for this purpose. Please see &quot;<a href="https://www.accesstoinsight.org/lib/authors/nanamoli/PathofPurification2011.pdf" rel="nofollow noreferrer">Path of Purification (Visuddhimagga)</a>&quot;, translated from Pali by Ven. <a href="https://en.wikipedia.org/wiki/%C3%91%C4%81%E1%B9%87amoli_Bhikkhu" rel="nofollow noreferrer">Ñāṇamoli</a>. It's a classic manual of Buddhist doctrine and meditation written in approximately the 5th century CE, and is considered the most important Theravada text outside the Pali Canon and its traditional commentaries.</p>
<p>It talks about the eight knowledges of insight:</p>
<blockquote>
<p>Now,  insight  reaches  its  culmination  with  the  eight
knowledges,  and knowledge in conformity with truth is ninth; these
are what is called purification by  knowledge  and  vision  of  the
way.The  eight  should  be  understood  as  follows:  (1)  knowledge
of  contemplation of rise and fall, which is insight free from
imperfections and steady on its course,(2) knowledge of contemplation
of dissolution, (3) knowledge of appearance as terror, (4) knowledge
of contemplation of danger, (5) knowledge of contemplation of
dispassion,  (6)  knowledge  of  desire  for  deliverance,  (7)
knowledge  of contemplation of reflection, and (8) knowledge of
equanimity about formations.</p>
<p>“Knowledge  in  conformity  with  truth
as  ninth”  is  a  term  for  conformity.So one who wants to perfect
this should make these kinds of knowledge his task, starting with
knowledge of rise and fall free from imperfections.</p>
</blockquote>
<p>The description of (3) knowledge of appearance as terror:</p>
<blockquote>
<p>As  he  repeats,  develops  and  cultivates  in  this  way  the
contemplation  of dissolution,  the  object  of  which  is  cessation
consisting  in  the  destruction,  fall and breakup of all formations,
then formations classed according to all kinds of becoming,
generation, destiny, station, or abode of beings, appear to him in the
form of a great terror, as lions, tigers, leopards, bears, hyenas,
spirits, ogres, fierce bulls,  savage  dogs,  rut-maddened  wild
elephants,  hideous  venomous  serpents,thunderbolts,  charnel
grounds,  battlefields,  flaming  coal  pits,  etc.,  appear  to  a
timid man who wants to live in peace. When he sees how past formations
have ceased,  present  ones  are  ceasing,  and  those  to  be
generated  in  the  future  will cease  in  just  the  same  way,
then  what  is  called  knowledge  of  appearance  as terror  arises
in  him  at  that  stage. ...</p>
<p>But  does  the  knowledge  of  appearance  as  terror  [itself]  fear
or  does  it  not fear? It does not fear. For it is simply the mere
judgment that past formations have ceased, present ones are ceasing,
and future ones will cease. Just as a man with eyes  looking  at
three  charcoal  pits  at  a  city  gate  is  not  himself  afraid,
since  he only  forms  the  mere  judgment  that  all  who  fall  into
them  will  suffer  no  little pain;—or  just  as  when  a  man  with
eyes  looks  at  three  spikes  set  in  a  row,  an acacia  spike,
an  iron  spike,  and  a  gold  spike,  he  is  not  himself  afraid,
since  he only  forms  the  mere  judgment  that  all  who  fall  on
these  spikes  will  suffer  no little pain;—so too the knowledge of
appearance as terror does not itself fear; it only forms the mere
judgment that in the three kinds of becoming, which resemble the three
charcoal pits and the three spikes, past formations have ceased,
present ones  are  ceasing,  and  future  ones  will  cease.</p>
</blockquote>
<p>The description of (4) knowledge of contemplation of danger:</p>
<blockquote>
<p>As  he  repeats,  develops  and  cultivates  the  knowledge  of
appearance  as terror he finds no asylum, no shelter, no place to go
to, no refuge in any kind of becoming,  generation,  destiny,
station,  or  abode.  In  all  the  kinds  of  becoming,generation,
destiny, station, and abode there is not a single formation that he
can place his hopes in or hold on to. The three kinds of becoming
appear like charcoal pits  full  of  glowing  coals,  the  four
primary  elements  like  hideous  venomous snakes (S IV 174), the five
aggregates like murderers with raised weapons (S IV174),  the  six
internal  bases  like  an  empty  village,  the  six  external  bases
like village-raiding  robbers  (S  IV  174–75),  the  seven  stations
of  consciousness  and the  nine  abodes  of  beings  as  though
burning,  blazing  and  glowing  with  the eleven  fires  (see  S  IV
19),  and  all  formations  appear  as  a  huge  mass  of  dangers
destitute of satisfaction or substance, like a tumour, a disease, a
dart, a calamity,an affliction (see M I 436). How?</p>
<p>They  appear  as  a  forest  thicket  of  seemingly  pleasant  aspect
but  infested with wild beasts, a cave full of tigers, water haunted
by monsters and ogres, an enemy  with  raised  sword,  poisoned  food,
a  road  beset  by  robbers,  a  burning coal, a battlefield between
contending armies appear to a timid man who wants to  live  in  peace.
And  just  as  that  man  is  frightened  and  horrified  and  his
hair stands  up  when  he  comes  upon  a  thicket  infested  by  wild
beasts,  etc.,  and  he sees  it  as  nothing  but  danger,  so  too
when  all  formations  have  appeared  as  a terror by contemplation
of dissolution, this meditator sees them as utterly destitute of  any
core  or  any  satisfaction  and  as  nothing  but  danger.</p>
</blockquote>
<p>Apparently, this will transition into a knowledge of peace:</p>
<blockquote>
<p>“He  contemplates as suffering<br />
Arising, occurrence, and the sign,<br />
Accumulation, rebirth-linking —<br />
And this his knowledge is of danger.</p>
<p>“He contemplates as bliss no arising,<br />
And no occurrence, and no sign,<br />
No accumulation, no rebirth-linking —<br />
And this his knowledge is of peace.</p>
<p>“This knowledge about danger has<br />
Five sources for its origin;<br />
Knowledge of peace has also five —<br />
Ten knowledges he understands.</p>
</blockquote>
<blockquote>
<p>Knowledge of the state of peace is this: “Non-arising is safety,”
etc.: this, however, should  be understood as said for the purpose of
showing the opposite kind of knowledge to knowledge of danger. Or when
it is stated in this way, <strong>that there is safety without terror and
free from danger, it is for the purpose of comforting those  who are
upset in their hearts by seeing danger through appearance as terror.</strong>
Or  else,  when  arising,  etc., have clearly appeared to a man as
terror, his mind  inclines towards their opposites, and  so this is
said  for the purpose of showing  the advantages in the knowledge of
danger established by the appearance as terror.</p>
</blockquote>
<p>So, the mind first sees the terror of the inevitability of the cessation of phenomena, and then experiences danger when it realizes that there is no place to cling to for safety from the inevitability of the cessation of phenomena. Finally, it accepts this situation, and sees non-arising etc. as safety.</p>
<p>Is fear not one of the five hindrances?</p>
<p>Well, if the terror of the inevitability of the cessation of phenomena, or the danger of no place to cling to for safety from cessation, hinders one from progress due to fear, then this falls under the <a href="https://en.wikipedia.org/wiki/Five_hindrances" rel="nofollow noreferrer">hindrance</a> of <a href="https://en.wikipedia.org/wiki/Vicikitsa" rel="nofollow noreferrer">doubt or uncertainty (<em>vicikicchā</em>)</a>, in my opinion, because the mind is doubtful and lacks conviction and trust, on whether it is the right way forward.</p>
<p>The same text states:</p>
<blockquote>
<p>It is without wish to cure (<em>vigatá cikicchá</em>), thus it is uncertainty
(<em>vicikicchá</em>). It  has  the  characteristic  of  doubt.  Its
function  is  to  waver.  It  is  manifested as indecisiveness, or it
is manifested as taking various sides. Its proximate cause is unwise
attention. It should be regarded as obstructive of theory (see
XVII.52).</p>
</blockquote>
 13992: <p>In a way, fear of annihilation is part of the five hindrances, for example:</p>
<ul>
<li>attachment to/desire for the continuation of sensory perception (i.e. to the physical body)</li>
<li>resentment/bitterness toward mortality</li>
<li>doubt in the concept of <a href="https://en.wikipedia.org/wiki/Anatt%C4%81" rel="nofollow noreferrer">Anattā</a></li>
</ul>
<p>Since individualism is a central tenet of Western civilization, it can be especially hard to anticipate 2 annihilations: the inevitable death of the body and the annihilation of self (the latter in Zen is called &quot;the Great Death&quot;) as a necessary step in attainment.</p>
<p>In addition, in Western culture we tend to &quot;hide&quot; death as much as possible, compared to Asian cultures. For example, there is a long tradition of monks meditating around a deceased person in Asia - not to mention the tradition of <a href="https://en.wikipedia.org/wiki/Sky_burial" rel="nofollow noreferrer">Tibetan sky burials</a>. You might say we &quot;push death away&quot; much more in Western culture.</p>
<p>As a consequence, we perhaps tend to &quot;push Anattā away&quot; in the same way we avoid being confronted with physical death (consciously or culturally). I struggled with this my &quot;self&quot;, until my teacher urged me to really mentally dive into what <em>really</em> discomforted me regarding this idea - and that's all it turned out to be in my case: the imaginings of what the actual event of self-annihilation would be like. Like what most people fear about physical death is not death itself, but the way it will come, I had formed the most terrifying scenarios in my head what this &quot;dying process of the self&quot; would be like. I would almost call it &quot;spiritual <a href="https://en.wikipedia.org/wiki/Hypochondriasis" rel="nofollow noreferrer">hypochondria</a>&quot; in my case.</p>
<p>Needless to say, all these imagined scenarios were completely absent from the initial glimpse of the actual experience (in my case through <a href="https://en.wikipedia.org/wiki/Koan" rel="nofollow noreferrer">Kōan</a> practice). But I did need that initial push from my teacher to dive into my extreme discomfort of the idea to get there.</p>
<p>Hope this helps.</p>
