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.
You can definitely do that. You can use Meshmixer to cut the parts and then glue them together after they are printed. Here is a link to a tutorial on how to do this: https://www.youtube.com/watch?v=1Wzut-W2zTk.
Meshmixer can be found here: http://www.meshmixer.com/download.html