Hi Stefan
My example was based upon very limited understanding, that the vertex colors are a property of the exported mesh, in unknown export format.
From Polygon mesh - Wikipedia:
"It is also possible for meshes to contain other such vertex attribute information such as colour, tangent vectors, weight ..... "

So the question is, can MoI geometry database contain colour information for the vertices, which could be exported in some format?
http://moi3d.com/forum/index.php?webtag=MOI&msg=8201.7
...but after the boolean calculation is completed MoI will decompose objects into manifold volumes and only put manifold objects into its own geometry database.

I'm in over my head :-)

- Brian

Edit, one last link, Rhino/Grasshopper related, not MoI:
http://grasshopperprimer.com/en/1-foundations/1-6/1_What%20is%20a%20Mesh.html
So MoI cannot do this...?