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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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You raise a good idea. But it doesn't seem to be just on the lower layers. I find my printer seems to "color just outside the lines" because I often cannot get interlocking pieces to fit. I thought it might be a characteristic of PLA but now I think my printer is a bit too imprecise.