BleepingComputer.com: System Fix- issues after virus is gone

So, I recently ended up with the "System Fix" virus on my computer. I ran rkill, which didn't help, but it let me run Malwarebytes using command prompts. The fake notifications have gone away, I'm relatively sure I got rid of the virus, and I now have access to my documents, music, etc (I ran unhide.exe) I also changed the setup to display hidden files. However, all of my program files still display as empty. Advice?

Thanks!

-College student. With a virus. During midterms.