3D scanners are great, but they create “dirty” meshes. Overlapping points and reversed normals don’t matter until you try to print the mesh on a 3D printer. Then the slicing engine will get confused because it can’t tell where the inside/outside of the model is. Correcting these “dirty” meshes involves a lot of tools, some expertise, and a little bit of luck.
Tony Buser has provided an excellent tutorial describing his process. He takes a 3D scan, massages it through several different programs, and the result is a perfectly printable 3D model.