Processing an stl scan

I have an stl scanned file of a blood vessel. I need to define the inlet outlet and the wall of the the scanned vessel but the solid has hundreds of thousands of facets.

I tried to merge the facets but I could only merge small patches of them most of the patches give an error when I try to merge them. I also tried skin surface which resulted in a small but unacceptable deviation and I need the exact geometry is there any other way I can use to obtain a solid?

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