Ok all might not be lost. Here's a quick fix if you have the same nasty malware virus. Some Malware hides your files they are not gone deleted just hidden from view.
First get rid of the malware using malwarebtyes program.
http://www.malwarebytes.org/ latest version is 1.50.1
Or unless you killed it with some other program good enough, open up any folder then in the menu go Tools - folder options - view. Then in the 'Hidden files and folders' check the 'Show hidden files and folders' box. Click the apply button below then the 'Apply to all button' up top. Applying to all means every folder will do the same, could take a while to complete.
Might not work if its more nasty than just hiding your stuff but worth a try.