Can't see nor launch programs on Start Menu

Hi. My computer recently prompted me to do a virus scan and after rebooting, it erased all the files and programs on it. I read some posts stating to "unhide" all the folders in windows explorer to help the situation. That seemed to restore alot of programs, but I still can't launch certain programs off the Start Menu nor can I see their shortcut in Windows Explorer. I'm able to open files using those programs from Windows explorer, I just cant open the program itself from the Start Menu. The folders of those programs on the Start Menu say "empty" and no program is displayed. Any advice?
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  1. What antivirus program are you using, if any?
  2. Uncheck Hidden on All Users profile as well as yours.

    That virus scan prompt was a virus itself. Watch what you install and run on the computer closely.

    Also run though the virus remove guide http://www.tomshardware.com/forum/8263-63-simple-free-guide-removing-malware
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