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MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I used Marlins m600 filament change at Z2.2mm, you can add it to the gcode with a text editor if your printers firmware has the advanced pause feature. The filament change is actually integrated into PrusaSlicer's preview tab too so I just added the colour change in there.

http://marlinfw.org/docs/gcode/M600.html

I can add a dual extrusion/mmu version today for people who can already print multi colour though