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.
I know this is a little late but I ran into the same problem, having all the parts grouped together. I went into Fusion 360 and sent all of the parts out to 3D print individually. it took a little bit longer on some of the groupings than I would have hoped, but it worked.