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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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Is that what you're seeing in the slicer? I made this in two parts (head was sculpted, shirt was modeled the old fashioned way with faces), but as long as your slicer is set to "union overlapping volumes", you should never notice this.