Normally, you don't need to do this----i.e. just open the file manager by double-clicking on a folder icon--or just open nautilus directly from the menus.
If you want to run nautilus as root (Do this with caution), then use "su" in a terminal and then enter "nautlilus". Even thought the rest of your Desktop is still running under your username, Nautilus will now be running with root privileges.
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