If the files are Hidden, try to do something like this
If they have been deleted, try Recuva, however if that happened you should see freed space.
EDIT: according to the comment, the problem might lie elsewhere, maybe the virus messed around with the files and placed them somewhere else. Use WinDirStat or some other disk usage statistics viewer to enquire about where most space has gone to.
EDIT + UPDATE:
To restore hidden folders to their original state you should do the following. Note that I'm on a Portuguese version of Windows XP, but the core is there, it should be transversal to Windows 7 or 8, and I'll make it as easy to understand as possible:
Assuming that you have a mix of non-hidden and hidden folders like the following...
...select them all, then press the right button on any folder, then go to
Properties. You can do the same from the menu bar but this way it's easier.
A window like the following will appear. Uncheck the
Hidden (in my version labeled
Oculto) checkbox, then press
If you are doing this from a NTFS Partition (most likely, unless these files are on an external drive) another window will appear asking if you want to make this change to ALL files, even those included inside the folders and those inside the folders inside the folders and so on.
The main disadvantage in doing that is that some system files (namely
thumbs.db will from now on appear even if you have the "Show hidden files option" disabled). If this bothers you, check inside the hidden folders if the files inside them are also hidden. If they are, it is less bothersome to allow this, unless you want to do this over and over again.
Lastly, the end result is something like this. All files have become unhidden.