The first step in our automatic landmarking scheme is to estimate an intrinsic coordinate system of faces scanned in 3D. For this we have developed a method based on the horizontal symmetry. This coordinate system provides an excellent basis for subsequent landmark positioning and model-based refinement such as Active Shape Models, outperforming other landmark localisation methods including the commonly-used ICP+ASM approach. 
These four images show the order of events :-
Once the coordinate system is established, a reference face, with known landmarks, is used to initialise the landmark positions. Then the method of Ruiz et al. [2,3] is applied to fit the landmarks to the new face.
Comparison of automatic and manual landmarking:
 WP Koppen, CH Chan, WJ Christmas and J Kittler An intrinsic coordinate system for 3D face registration In Proc ICPR, 2012.
 MC Ruiz and J Illingworth Automatic landmarking of faces in 3D - ALF3D In IEE International Conference on Visual Information Engineering, 2008.
 MC Ruiz Automatic face landmarking in 3D PhD thesis, 2011.