MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I am also facing the same issues, but these are mainly caused by the printing rather than the design. For example the socket on Rail1 is supposed to be 9.41mm but the actual print measured as 8.8mm. So there is some shrinkage, but unfortunately not everything shrinks the same, so my parts still don't fit :( However the entire rail length is still correct, so it seems only the joints shrink.