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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One way is to not left the head of the screw flat when retracted. At least at my printer if the head is 2mm out when retracted it stills higher than the nozzle. This will render a longer probe when released and could help.