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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I just printed another in PLA on a raft sliced in the new version of Makerware and I have no fit issue and it snaps just fine. Out of curiosity are you using PLA or ABS? What slice software and what bot? Since I proofed the design in PLA it is possible that with the greater shrink value of ABS the case is too small in that material. In that case the easy solution is to simply scale the file in the x and y axes by a half a percent or so and try again. Since I am not able to replicate the tight fit issue my other suggestion would be to check your calibration with a test print with both internal and external features.