It’s possible that your infection was bogus antimalware and has hidden the files.
1.Read about and then run Unhide, scroll down here http://www.bleepingcomputer.com/forums/topic405109.html
2.Alternatively, type these commands to reset the attribute (the capitals are for clarity only, but note the spaces in the commands):
Open a Run window (Windows Logo key+R), type CMD and press Enter. Type C: and press Enter. Type ATTRIB -H /S /D and press Enter (this may take some time). Type EXIT and press Enter.
After resetting the attributes, you may have to hide the system files. To do so, go to Folder Options > View Tab and put a tick in Hide protected system files.