I am now a co-author to the geometric morphometrics digitizing and analysis software in R, called geomorph. For a detailed look at what the software does, take a look at the CRAN pdf or this paper. In brief, the software package is designed to be used for digitizing 2D and 3D landmarks, and implementing many of the common (and some not so common) procedures and statistical analyses with these data.
Digitizing of landmarks and sliding surface semi-landmarks on three-dimensional structures was already implemented by my co-authors, using the vertices of 3D surface models (e.g. ply models). I have improved these existing functions to take full advantage of the enhanced plotting capabilities of PLY files with rgl (the ply files are read in and stored as objects of class Mesh3d) . Now the digitizing experience is more user friendly; the color detail of the meshes and the plotted faces allow better visualization of complex meshes, and the software is now compatible with functions in the Morpho R package. We welcome users to try out the new digitizing functions and tell us what they think! You can send me a message here (right) or visit the geomorph blog page.