You can remove popups or menu items using the same method: use RemoveItemFromMenu specify the name of the menu and the name of the item.
Note You can only remove items that you have added. For example, System Architect menu items cannot be removed. The items are not actually removed, they are instead hidden. This allows users to customize the items to be elsewhere in the menu system. Note you can specify "" for the Menu name, as the Menu name is now ignored. The item will be hidden wherever it is in the menu system.