Amrap: If you have the plywood lightly tacked to a framework, you have to watch on the cookie cutter that you don't run the jigsaw into the framing members.
Generally, with cookie cutter you expect to leave the unraised bits down at elevation 0. BUT there's no reason you can't use cookie cutter variations 2b or 2c where bits of flat board are removed.
There is a further variation where all that's left is track bed and some outside walls and the scenery is suspended in the middle.