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As it is the only way to activate transparent themes in Gnome-shell(to make it look good), How to disable nautilus from handling the desktop and can i make it handle the desktop again and what will happen to the unity and desktop icons and how to handle the desktop icons without nautilus???

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You should remove the file /etc/xdg/autostart/nautilus-autostart.desktop (or at least modify the OnlyShowIn line into it).

Then you should always run nautilus with the --no-desktop option (this could also require to modify some menu item or quicklist).

You can manage the desktop with nautilus again at any time launching nautilus without the option --no-desktop.

To manage the desktop in an alternative way you could look at some other file manager.

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Works well.But i was shocked when opening Unity-DE that desktop icons still there, i was thinking that disable nautilus from handling the desktop will happen to all DE-s(i,e, nautilus still handling the desktop in unity and not handling the desktop in Gnome-shell and it is great) – Naruto Dec 3 '11 at 20:19
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If you install the gnome tweak tool (which you'll want anyway) you can disable file manager handling the desktop. But as far as I know you will then have no desktop icons. Most if not all DEs are structured such that the file manager handles desktop icons.

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