The other day I had to clean a laptop from a virus that:
Hid all exe's
Didn't let me go to folder options, show hidden files/hide system files
Created links with the names of the exe's it hid
Unabled the antivirus
Infected any external storage device you plugged
Didn't let me run command prompt or task manager
Didn't let me restart in secure mode
What I did (after a lot of banging my head on the desk):
Searched in that quick search bar in Win7 explorer for *.exe
It found the execes and executed Elistara (Awesome just-run antimalware tool)
It enabled the task manager and command prompt
I ran the command pront and executed drive:> attrib -h -s -r /s /d (remove hidden, system and read only attributes of all files including directories and looking inside subdirectories)
Ran Avast (great for reboot scans) and Malwarebytes
Deleted those pesky direct links manually (searching for *.lnk)
Installed panda usb vaccine (it disables automatic run for external devices to avoid infections both ways and writes an unwritable autorun in the external devices so no virus can overwrite it)
I hope this helps someone.
Edit: For those saying "Stop using windows"