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I got the following model: http://doekewartena.nl/temp/sw_test01.obj

Which is kind of crazy. When I upload it to shapeways it tells me it is not manifold and it is unable to repair it.

I did remove all doubles. I fixed the holes I could find. I did the check with the 3d printing add on and there it is manifold. So now I have no clue of what to do next.

Is the model just to complex itself?

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I think you might have to consider on retopology. It will fix manyfolds, and will simplify your model. You can even try just to decimate the model. For automatic retopoly, you can try "instant meshes": https://github.com/wjakob/instant-meshes

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Non-manifold doesn't necessarily mean double vertices (although there are quite a lot in your mesh). It could also mean that you have vertices inside your mesh. Import it into blender, tab into Edit Mode, then go to "3D Viewport - Menu - Select - All By Trait - Non Manifold". Try to delete the vertices and then try to verify on shapeways again.

Your second question: I don't have much experience with printing, but I think your model is way too complex and it also contains ngons.

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