Cant see program files in 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. You mean a webpage promted you to do a virus scan LOL
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