Hi dnm, so also I took a look at your second file dis3-joined-solid.3dm and that is better with not so many individual surfaces but the bottom piece has open edges along its outer border.

Your best bet would be to make the whole thing as just one single solid unless you have some special need to do otherwise.

Some solids modeling programs don't like to work with anything other than full solids where there aren't any unattached edges at all. I don't know if Atom3D is sensitive to that or not.

- Michael