MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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Sorry I don't have the ability to modify the parts like that anymore as I don't have access to the same CAD package anymore. Probably easier for you to just import the STL into something, do a cut of the ID you need, and then save the STL back out again. My other idea is, print the parts, and then bore them out to the size you need.