Hi Danny, MoI does try to get rid of non-manifold edges after doing booleans, but the main way that it does that is by breaking things apart into separate solid regions so different volumes that have common edges between them become separate objects. But that does not handle this type of situation you had here.

The non-manifold edges will probably become naked edges after you save such a thing out to a file and read it back in again, much of the stuff for going into various file formats including 3DM expects the model to be manifold.

- Michael