I recently was infected with Vista Antivirus 2011. I ran spybot, and it seems to have taken care of the malware, but when I look at Windows Explorer, all of my files are gone. I still have software in my program files, but all of my documents and files on the hard drive are missing. I downloaded Spyware Doctor and am running the scan now, and it is scanning all of my files that do not appear in windows explorer, so it seems like they are still there, I just can’t see them. Any suggestions?
Duh! 
It worked, thank you!
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on: 1st January 70
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The virus most likely hid them, in windows explorer, press alt, then go to tools then folder options and click on view then look for show hidden files and folders. check that box and press ok.
You are better using the free scanner from http://malwarebytes.org. It actually normally fixes these problems as well as removing the infection. Spybot is no longer a good option, nor is spyware doctor. If you still can not see the files they are hidden. You need to be careful here, it will require going to each folder in turn under the C: drive in computer and from Organise/Folder options/View turn on viewing of hidden AND system files. This will raise a warning. Then go to every folder and make visible your stored files, favourites etc. Do NOT set system folders visible or you risk changing or deleting them which can trash the system. Then turn OFF viewing hidden and system files.