I worked few times with pure mesh on rhino.
I think (but i am guessing) that usually you try to clean the mesh with the software that created it, like the 3d scan software, or what was used in this case (x-ray?).
I don’t know how advanced are rhino tools to do this kind of “clean up” with meshes…
I really liked meshmixer, when i needed.
Maybe try to use the select by brush tool in rhino, then make a rough cap (even triangulated), then quadremesh will pass over everything and be better. Probably.
Another way is to use WIP version and try shrinkwrap command, but I have never tried it yet.
This way How to smooth a curve but preserve area? - #3 by DanielPiker