There is a freely available MATLAB codes for smoothing arbitrary surface objects using spherical harmonics. It's a different technique. But this technique will provide surface-to-surface alignment automatically without additional computation. See
http://www.stat.wisc.edu/~mchung/softwares/weighted-SPHARM/weighted-SPHARM.h...
You may have to change code a bit since "mesh connectivity" will be different from one surface to another.