Cleaning up a 3D scan with Meshmixer is easy. Alternatively use Blender for a more manual procedure with more control.

1. Import & orient the model upright: Edit > Transform.
2. Cut away unwanted geometry: Edit > Plane Cut.

1. Join the disconnected sections (blue lines indicate boundaries): Edit > Close Cracks.

1. In Select mode, click anywhere on the part you want to keep.
2. Expand the selection to all connected vertices: e.
3. Invert the selection: i.
4. Delete the loose parts: x.

1. Save your project(!)

1. Make the mesh solid: Edit > Make Solid.
   1. Set the solid type to Accurate
   2. Increase Solid Accuracy and Mesh Density until you're happy with the result. Press Accept.