How to have bottom side up terrain collision?

In my game, in a attempt of creating a dynamic destructible terrain. I want to use typical terrain meshes/unity's terrain builder as essentially a mold for game objects that will actually be the destructible dynamic terrain. So instead of manually scripting or placing these objects in the way I want the terrain to be designed. I wanted to use the standard terrain designing tools(unity terrain, 3rd party 3d modeling) then take the terrain mesh and use it as a mold to position my rocks/game objects procedurally somehow. Then I'd remove the terrain mesh and hopefully the game objects should have the same topography as the terrain. I have tried filling the game objects onto the terrain from the topside. But the problem with that is that the more layers of destructible game objects the topography of the terrain would disappear.