Is not that hard to separate the upper teeth and lower teeth as different objects.
Here is the workflow (asumming you are using Blender):
1. In Edit mode (Wireframe view) - Brush select ([B][B]) some vertices from the neighbouring surfaces (head, tongue, gums etc.)
2. Press [Ctrl+L] to select all linked to the selection vertices, then press [H] to hide them.
3. Now when the upper and lower teeth are only visible, brush select some vertices from the bottom teeth and [Ctrl+L] to select the rest.
4. Press [P] to separate the selection as new object.(Now you can Box select the upper teeth and separate them too).
5. You can unhide the hidden parts by pressing [Alt+H]
It will take less than a minute