You might also make a group of a group, before exporting to modelmaker, this tends to be cleaner, without the wayward points. i.e. make a group of your desired surfaces, call it group 1, then hide the surfaces, leaving group 1 on its own, select this group and use this to create a new group 2.
You could then mirror this group to port and starboard before exporting to modelmaker.
Make sure that all surfaces are joined or trimmed before making the group.
In modelmaker there is a button to remove excess points. You may have to do some fine tuning manually.
Another approach is to make separate gf files for the hull and appendages, but I don't know how this will work for the CFD
Hope this helps.