Editor-in-chief sent an email to resubmit my manuscript I've submitted an article to an Elsevier-based journal and after one month, 
an email has been received from Editor-in-chief stating: "Please upload figures separately from manuscript and resubmit it as soon as possible".

What does the email mean?

What will occur after resubmission?
It means that you should resubmit the manuscript with figures separately, as it is probably stated somewhere in the journal's instructions for authors.

They probably cannot deal with the formatting otherwise, and depending on field and journal I would say that it is quite likely that your manuscript has not yet been reviewed, as stuff not living up to guidelines tends to go to the bottom of the pile.