Post-Virus repairing question?

So i got rid of a virus/anti-malware thing that made my computer screwy, and it had shown all my files and programs as hidden, even though when i plug in a zune the zune program shows up still, and when i save a picture to my new blank desktop window, i can still edit with GIMP when i right-click it. i got rid of the virus, but all my files are still showing as not existing, even my dell desktop bar. how can i "unhide" this?