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MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I ve the same issue. On the last 2 steps there is excesive material due to the infill and the nozzle mess with it.

At first I supposed its a matter of high or infill area so i printed a single column of 25x5x5 mm and it printed it perfectly.. so im running out of options... Any ideas would be appreciated. (ps: Im using slic3r)