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 didn't pause it at all. As its printing, I simply pull the filament out and put in the new color filament. I can do it quickly enough that it doesn't effect my prints. There may be better ways, but my printer doesn't pick up where it left of very well after pausing.