The programs I use to make templates for EVA foam are a mix between Metasequoia and Blender
And to exemplify a process that if I do I will use the stl of the ODST viewer that is in the forum armory
And to adapt an STL model what I would do is import the STL model to Blender and pass it to OBJ to work on it in MetaSeqoia since it leaves the files almost directly for use in Pepakura
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Metasequoia has tools that allow you to simplify the models, although if you can apply this process in Blender much better
The mesh of the STL is usually very heavy for Metasequoia due to the number of polygons it has, preventing them from loading well and in the unfold, releasing many triangles that are very tedious to join
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and if it is about reducing the mesh, it leaves a disaster of polygons in the model
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One of the advantages of MetaSequoia is that it allows you to work on an existing mesh by being able to superimpose new faces on a high-poly object (just make sure to create the new faces on a new object)
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Once you have a mesh that you like the way it looks and is simple, you can apply a mirror effect to it and with the edit tools modify the mesh to join the mirror object with the normal one
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Once you have the mesh like this you can add or remove axes with the Edge tool (W)
in this way being able to add details that the model has in high polygonage
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With the letter E on the keyboard, you can highlight those same details
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Once you have a result that you like you can do the other side of the mesh by hitting SEL OBJ, selected, mirror and select the axis that fits best
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Once you have the object mesh complete, I do recommend joining edges by hitting Object, Join Closed Vertices, and setting the value to one that does not reduce the polygons
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And so you would get a model comfortable enough to work in pepakura, it is a bit tedious and time-consuming to make them since they do not always come out the first time, but it assures you that it is possible to work it in EVA foam and even in the papercraft mode
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I saw that manual conversion trick from STL to EVA rubber template in this video (which does it directly in Blender)
Another very easy way is to look for the model in the form of a Game Asset since it has a reduced mesh and at the same time it already has the same separate ones, which is usually what I do