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MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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first thing you can start with is making sure the filament diameter is correct in the slicer, then esteps, then the extrusion multiplier. Most problems with print-in-place objects start with the incorrect extrusion multiplier; if the parts are stuck together your ex multiplier might be to high. Your right though it can be daunting to figure out the exact variables to why your prints aren't coming out like they should but you can rule out a lot of them buy just observing your printer print. The parts are fusing together; you're extruding too much filament; what settings control the amount of filament being extruded?Filament diameter, esteps, and extrusion multiplier(there are some more but these are the main ones). That doesnt work what else can it be? Maybe there's big blobs at the end of my loop causing layers to fuse so i need to increase the retraction. My point being is depending on the situation you can rule out 85% those variables leaving you with 15% of guess work.