Start Menu Programs appear "empty" after virus scan

My antivirus software prompted me to do a virus scan and after rebooting, I was no longer able to view any of my program files nor documents. I looked up at some posts and found that I had to one by one uncheck the "hidden" tab on the folders in the system. I was able to retrieve most of the files and programs, but not all of them. I still have a few programs that appear as "empty" on the start menu (i.e. Microsoft Office programs). Any other steps I should take to be able to launch all my programs in the Start Menu?
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  1. Which antivirus program is this? Sounds dodgy to me.
  2. Avast said I had a "Trojan" and it said to perform a full scan. After I did, it said to perform the "full boot scan". Computer rebooted then it showed the Windows7 Repair on the middle of the screen and I clicked it. Then the computer rebooted and everything was wiped.
  3. sounds like you got the "Windows Defender" lookalike virus. It looks like a Windows Defender popup, but it isn't. You can tell because they send you to a website asking for credit card information. There are also some spelling mistakes if I remember correctly.

    What that virus does is it makes all your files invisible. You have to remove the virus first, and then you have to set all your files visible again.

    Before doing anything you should identify exactly what popped up.

    Generally the procedure goes something like this "Go to this site:… and download the rkill.exe file.

    Then go to this site:… and download the Malwarebytes Anti-Malware tool.

    After you have both of these files, run the rkill.exe utility, this kills all known forms of mal-ware anti-virus programs. DO NOT RESTART!!!

    Now run the Malwarebytes Anti-Malware utility. Have it do a quick scan, this might take about 5 minutes. Cross your fingers that it finds some errors. I think it will. Allow the program to delete these mal-ware it finds. "
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