I want to remove the following shortcuts from the preferences menu from terminal. Main Menu, Remote Desktop & Apperance. Can anyone help ?
for every user
if you want to edit it for everyone, then you can move desired .desktop files from /usr/share/applications directory, in your case alacarte.desktop, vino.desktop and gnome-appearance-properties.desktop
for one user
if you want to edit it for one user, you will probably need to edit file .config/menus/settings it is xml file. So, adding desired_file.desktop in second ... part could do this. Im not so strong with explaining how to edit xml files, but you can see what you will need to add there if you will look what changes when you will disable something in alacarte ( gui for editing menu )
Here a GUI way to do it. Open Alacarte . (I think it's installed by default on Ubuntu).
It's very intuitive and easy to use. You can enable/disable any element.