I recently encountered a virus that hides everything on a hard drive via the attribute +H. The result is: No start menu programs, No desktop icons, No visible files or folders in Explorer. The latest version, deletes all shortcuts from the allusers profile, which will require some grafting work. The same will also set some files and folders +R. There's a few utilities on the web that can "unhide" all files and folders. Here is one more with some control over "what" files/folders it hides