Need to remove internal Faces within a surface

I have a color 3d Systems printer which is printing with powder. I am trying to print a a map of a county which is covered with hexagons of different height. The print consists of say 400 hexagons covering the map.

The problem I am running into is that with the software I have (3D Edit Pro that came with the printer) combines some of the hexagons into larger surfaces (sort of like tetris shapes), so I end up with a composite of objects containing multiple hexagons attached to each other. The software leaves the internal surfaces between the hexagons, which appears to be messing up the print. I need to go in and remove these internal faces between the hexagons to create a hollow surface for each object in the print. This is very time consuming.

Does anyone know of software that would remove these internal surfaces? If I could interpret the model file, I could write code to remove these myself, but I would prefer to use an existing app if possible.

You can open your stl for the multi-hex model in MeshLab and use Filters > Cleaning and Repairing > Remove Duplicate Faces.