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.
My Ultimaker has a similar feature, I haven't actually used it yet. It is great for color changes like this. Can also be used to add an external object in the middle of the model. Things like magnets, tumbler in a whistle, or other permanently embedded goodies.