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baking high-resolution mesh … 3; in which we clean up geometry

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Before we proceed to building a proxy geometry, we need to clean up the stl file. In particular, we need to separate the skull and jaw into two distinct geometries, while maintaining that they have no holes – ie. that they remain watertight.

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A useful tool to find bridge connections is the select connected command, or whatever it’s called in your software of choice. One method is select all connected which will show that they are connected, and the grow method of selecting neighbors, which helps pinpoint where the bridges are. Above is an example of this grow method as the polys connect across what we would wish to be distinct geometries.

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Now that you know where the problem area is, you can get in there and select the connecting polygons and delete them.

Note that there are many ways to do this – a truism for all of the steps in this process, and its generally advisable to build on your skillset. A programmer, for example, can code and might understand mathematics. So she might write a script that selects polygons based on an occlusion algorithm. I, on the other hand, can shovel. So I go in there and dig out one poly after the next, in glorious hands-on intimacy. 3D has something for everyone, and you’ll surely be bringing your own skills to the table.

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You’ll undoubtedly run into single shared vertices… thinking a full edge has to be shared in order to unite the two meshes, but no… such is the injustice of 3D clean-up.

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Eventually you’ll achieve that satiating moment when – upon double-clicking to select all connected – only the skull or jaw lights up. Enjoy it…

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… because now you have to climb back don into the trenches, closing all the holes you’ve just made. Make that look like…

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…this. Over and over again. It goes by rather quickly however.

 edit:
Forgot to mention that:
>finding holes is quickly done by selecting boundary edges. If this isn’t supported by your software, select edges with >4 poly associations, this will often >fillin
g the holes can be done easily by selecting edge, creating poly and triangulating. This maintains stl support for future printing etc. You can also bridge using an extrapolation of the edge poly’s normals, which maintains the anticipated surface shape in cases where the hole is so large that the first technique would result in a flat dent. Both techniques are likely within the range of acceptable deviance.