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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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That is a bit more complicated. You need the most recent files if you want to use stepper motors with four mounting holes or 40mm fans to cool the steppers. Other that that there is no difference, you can combine them as you want.