Can you give an example?
Only system files should be hidden and even that can be changed with windows explorer settings. Organize ... Folder and Search Options ... View tab. Show hidden files, folders, and drives. Uncheck Hide empty drives. Uncheck Hide protected operating system files <- if you do this one, you may start seeing files in folders such as desktop.ini. Although desktop.ini is safe to delete (it simply holds the display structure you picked for this folder) there are other system files you should not delete.
Windows 7 will also lock files such as My Documents, etc. These files are part of the Libraries structure and so W7 tries to control how they are accessed. W7 tries to keep you from going directly to c:\Users\YourUserId\My Documents because it wants you to use My Documents under Libraries instead. This can be overridden with the
Take Ownership script if you require less W7 controlled access.