Can you be more specific? If you're analyzing the same kind of bones you should use the same landmarks. Otherwise, the standard of your comparison will be controversial.
I do not really understand your question but maybe the following might help:
Co-registration of point clouds or meshes can be done with a free tool called CloudCompare: http://www.danielgm.net/cc/
Cloudcompare has an ICP (+ scaling) algorithm to co-register two 3D objects (meshes or point clouds) and you can choose from various algorithms to compute and visualise the differences between them.
Also, the free Meshlab can do point cloud comparison: http://www.meshlab.net/