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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The secret is Prusa Slicer. It's got an unload and reload feature for layered colors. By the way Slic3r or Prusa Slicer will work with other printers. You just have to correctly configure the slicer to get the correct GCODE.