1a) practice some manual retopo method (it`s bullet proof but time consuming) : https://www.youtube.com/watch?v=BEwEWKOH5ws
If you will want sharper edge you should do smaller polygons or add additional edge loops.

1b) use quad remesher in Blender - https://www.youtube.com/watch?v=p_iLzSWMbP8 or InstantMeshes software.

2) import quad cage as subd to MoI3d. MoI has better subd>nurbs convertion than Rhino (IMHO)

If you will do proper retopo work you will loose mesh errors from scan. Surfaces will be much cleaner.

One additional note: some surfaces made in that way might be too dense and have too many control points to be well thickened or edited in Alibre. I`ve tested few parametric cads on some surfaces made in this way and this is not so simple answer. Best would be old school traditional surface built from low count of CP. Dense CP surface = problems during edition (thicken and offset may fail sometimes).

Please give some tips if you will find is it working for you or not.