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 got the magnets from Fry's Electronics. They are the 8mmx3mm ones. That leaves a millimeter or so of wiggle room, to allow precise positioning during the glue-up phase. Here's the page: http://www.frys.com/product/7309494