How to make a 3D map?

Im wanting to make a 3D map (for a war-table) where mountains are 3d and sea is flat. Ive used the Displace mod with clouds to create the mountains. How would I flatten out the sea areas?
The below is what im wanting to achieve.

[THIS POST HAS CHANGED FROM THE ORIGINAL AS I FEEL MY METHOD MADE IT MORE DIFFICULT FOR MYSELF]

There is only so much that can be done when modeling with poly, you can try a quick clean up after using boolean if what you want is clean-ish mesh for the plane.

After the boolean try X> Limited Dissolve

If you used painted vertex weighting with the displacement modifier, then you should be able to use the same vertex group with the inverse toggle and use the shrinkwrap modifier to set the level of a flat surface. Then you just need a plane object to shrinkwrap onto for the ocean level.

I hope that makes sense, and I’m sure there’s other ways to do it too. But that’s what I could come up with off the top of my head.

The classic way to do mountains is with proportional editing to “grab” pieces of a flat surface and “pull” them up. Just prod and poke the thing until you get it right.

But you might also consider making the mountains one object, and the sea another.