MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I think in both cases you may be importing the models into your slicer, thinking they are in METRIC units(millimeters), when in fact they are in Imperial units (inches). If that is the issue, scale the part up, in your slicer, by a factor of 25.4. (1 inch = 25.4 millimeters exactly).