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.
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 anywayhttps://www.prusaprinters.org/color-print/
just upload Gcode and tell it which layer to change and it does the rest ;-)