MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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Even with high quality smooth rods, misalignment can require some force to lift the carriage. Also, does your printer have the threaded rods supported by the motor bearings through helical couplings? This is a very common but horrible design because the flexible couplings act like springs in the Z direction. Any binding in the Z axis will cause the couplers to compress (or stretch) giving you an uneven Z height.