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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i used the "change filament" option on my prusa it doesnt work perfectly everytime though.
you might be able to used prusas colourprint website ... worth a shot anyway
just upload Gcode and tell it which layer to change and it does the rest ;-)