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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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Personally I only had this when Z hop was turned on to 0.3mm or greater. It seemed that the layers were getting squished together, and the objects did actually get about a millimeter shorter, though reducing hop to 0.2mm solved this entirely.