I have no idea what you are up to - but would Agisoft PhotoScan (see http://www.agisoft.ru/tutorials/photoscan/03/) be an option?
You should have a look to CloudCompare, it is an open source sw useful for comparing objects - points model vs points model, or points model vs mesh.
Claude, you should explain a little bit more to let us understand about your data, basically any GIS software (ArcGIS, GvSIG, GRASS, ...,) would be usefull if you have DEMs o 2D layers. On the other hand, if you have point clouds or 3D data I would recommend you the use of a specific software such as CloudCompare or similar.
If you are interesting in morphometric you should try the software landmark: http://www.idav.ucdavis.edu/research/EvoMorph. It is a freeware which one you could put landmarks, export data and after that analyse them on a statistical software like MorphoJ.
I hope it could help you.
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