Model alignment

[manjula (Manjula Herath)]

I think you can do that with good accuracy with the 3D Slicer.

Have a look at SlicerCMF tutorial here.

3K Surface Registration

If it does not work you can do get it to work with the SlicerIGT fiducial registration

@lassoan

If you can accurately identify landmark points then you may use Fiducial registration wizard module (in SlicerIGT extension) to register based manually placed landmarks. See U-12 SlicerIGT tutorial for step-by-step instructions.