Are you using Gnome or KDE?
I'm unsure about KDE, but I know they've locked the Gnome menu as read only.
usually you would point nautilus to applications:/// and edit it from there, now you have to do things in a bit more complicated fashion.
Now, you have to go to /usr/share/applications
There are a lot of *.desktop files. They are the actual links under the menu.
You will have to edit them with whichever editor you use.
A good starting place on how to do this would be
here
For KDE, or XFCE, that's a whole other story. Good luck