Software: Cloud Compare for point clouds. Meshlab for meshes. Those are my go-tos. But it then comes down to how you want to present/visualize the data.
If it's very flat (surface of a painting changing over time), instead of dealing with 3D geometry, going to digital elevation models (basically quantified depth maps) might be better. The results are basically images and if aligned they can then be compared in photoshop or other programs.
Yale had a similar project that I was involved with the capture but the processing an analysis dragged on after I left so I am uncertain what came of the project I haven't seen anything published: https://news.yale.edu/2014/02/19/many-faces-alexander-pope-illuminating-art-history-through-digital-imaging
I also recall at some point a study of the Jean-Antoine Houdon Benjamin Franklin busts, but forget where that was published.
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Kurt Heumiller
3D Photographer/Coordinator
National Gallery of Art
Arlington VA
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