MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
Either smooth both halves before pressing them together or use something to fill in the gaps. You could smooth them out with a very fine grit belt on a belt sander. You could also use XTC-3D to fill in the gaps.