I am looking for an open source alternative for GeoMagic, that can do alignment of 3D meshes using a fit algorithm and analyse the difference between two point clouds. Any ideas are welcome - thanks!
You should also look at CloudCompare. For what you want to do, I think it is easier to use than Meshlab and have better reporting capabilities for mesh to mesh difference.
You can use our software Checkpoint (below) to collect 3D landmark points on surfaces and perform some 3D shape analysis. For example, you could collect a large set of points covering the both surfaces and compare (and/or average) them across specimen.