Actually, something that can be helping is using a 2D zone under the 3D terrain. You can then remove the 3D piece(s) the time to move your miniatures without changing the emplacement of where the terrain "counts" in game terms. And then put it back so that it became "pretty" again.
Very useful for terrain zones like forests (if you like to play a "real" forest with many trees close to each other, not the Citadel one).