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 with the .stl is very easy: You create two .stl files of which each contains the part that is printed in one of the colors. In the slicer you put them exaclty on top of each other and assign them to the different extruders.