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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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It's easy... please read the instructions provided on Thingiverse again. All you need to do is pause your machine at the appropriate time, swap filament colour, then resume your print. Once you've done it one time your future prints are sure to become colourful in the future!