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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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I am using an ultimaker and slicing with Cura. I had the same problem with the rockets being not completely flat. I easily fixed this by using the "Cut off object bottom" feature with 0.5mm setting.