I got some really cool models that were created from medical imaging data.

3D Printing
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I got some really cool models that were created from medical imaging data. Unfortunately they have lots of “foam” due to the thresholding algorithm used to create the original mesh. I’ve been trying to clean this up in blender (see linked thread), but it is very slow and tedious. Does anyone have suggestions for how to smooth this down, remove any “bridges” coming out from the main surface, and get it into a suitable state for printing? I’m looking for free mac/linux/online tools.
https://blenderartists.org/forum/showthread.php?411366-Removing-thin-spiky-3D-noise

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I am not familiar with blender, but if it has erode and dilate functions you should be able to use a sequence of those to remove and add volumes which will tend to destroy the spiky protrusions. If that wont work you might be able to load the model or original data in an image analysis program like Fiji and accomplish the same thing. https://fiji.sc

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Blender has some sculpt tools that sound like your erode and dilate, but as far as I can tell they won’t erode completely through a mesh. So I’m left with extremely thin versions of the bridges above. Likewise for smoothing/flattening tools; I end up with a bunch of coplanar layers, half of which have the wrong normals

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Unfortunately I don’t have the original data (unless Fiji/ImageJ can load STLs?)

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@Spencer_Bliven I’m not sure as I only use it for 2D image data, but it might. It is worth looking as it is free/open source software.

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Try using the “Make Solid” tool in Meshmixer. If you want to use a tool that will get rid of them, any of the Meshmixer sculpt brushes with refinement and reduction turned all the way up will remove them.