Is it acceptable to modify the format when republishing an article? My faculty has asked for permission to republish one of my articles. This is planned to appear in an upcoming magazine within the school I am currently working in. I have already asked the permission for republishing. It is an IEEE article, but I have some issues about the new printing.

The person in charge of the magazine has told me that they need the change the format of the article, so that it is according the magazine standard. Anyway they plan to change the following things:

- size of the font
- convert from two columns to one column
- referencing of the tables and graphs in APA style (I think IEEE uses another format)


But the content would be left unchanged. I have seen that in the Certification of Clearance sent to me by IEEE states the following:


  All uses not specifically authorized in this license and specified in
  the options for reusing IEEE Licensed Material available through the
  RightsLink service are prohibited, including (i) altering or modifying
  the Licensed Material in any manner


and in other part it says:


  If the Licensed Material is altered or modified in any manner, it must
  be within the scope of the license granted and it must not alter the
  meaning of the Licensed Material or in any way reflect negatively on
  the IEEE or any writer of the Licensed Material


So according to this, can they change the format? 
Thanks
There are many types of rights related to intellectual property, and it is important to understand them correctly. The one you're dealing with here is copyright, which covers the text, graphics illustrations, and other possible graphic media (video, if your paper include any).

However, the copyright which you transferred to them does only cover these elements. Once they give you permission to reproduce the text and graphics, you can reproduce them in any way you want, following the license. But the presentation (fonts, page layout, etc.) is not part of the copyrighted material.