If your using Nautilus File Manager you can create a file called '.hidden' in the directory where you want to hide files, open it with a text editor, and add the names of the files you want to hide (with each files respective extension as well).

This is not an system wide automatic method of hiding files without renaming it (in Linux files and folders are automatically hidden if they have "." in front of the file/folder name). You would have to do this manually for every file/folder that you want to effect; and only feasible for the Windows system files/folders that you really want to keep hidden and not want to mess around.