Files can be hidden individually, or as part of a folder (or entire folder tree) that's hidden. The OS may also treat "system" files as hidden.

To see *all* hidden files, click to "Tools/Folder Options/View" in Explorer (not Internet Explorer, but the tool you use for navigating your hard drive.) Check "Show hidden files and folders," and UNcheck "Hide protected operating system files." (I also like to UNcheck "Hide extensions for known file types.") Click the "Apply to all folders" button at the top of the Window, and then you should be able to see all hidden and system files and folders, everywhere on your hard drive.