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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.

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If you load the models in Autodesk Meshmixer (free), you can simply press "s", then select a part, press "e" to expand the selection and then "y" to separate it from the rest, so it's quite easy to separate it. I 3D-printed the units lying 30-60° on their back so most of the support was from behind which worked really fine for me (I have a single material printer).