ofcourse.
On the underside of your ship, create the shape that you want to cut out. Then, use the Push/Pull tool the make a bigblock that is as long as you need to go past the endge of your saucer. If you deselect the Show Hidden Geometry option, you can then right click on your saucer, select Intersect with Model, and then you can delete both the box and the part in between the lines where the box originally went through your hull
