Libraries, Homegroup, User, Computer, Network, and Control Panel are showing up under Desktop in windows explorer. I recently removed the fake system malware virus, which just refused to die. Everything works, but I really don't want to have to reinstall everything if I can help it.
What I want to know is how to move all the system folders back where they belong.
Definitely DO NOT do a Windows System Restore. You should delete all your Restore points, or you may accidently reintroduce the infection.
Run a sfc /scannow or repair-install the OS from CD.