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yes you can start with ports on a head that have been digitized. Then use that digitized model as your "blueprint".
A good machinist/programmer will go in and alter that model to make it better. Then keeps changing it as the data comes in and logs the data to what works and doesn't to better the head.




My exposure to digitized/3D scanned parts begins as a point cloud file that is then converted to surfaces. My life would be much easier if I had CNC machinists that were skilled enough to modify surface data. Guys like you are few and far between.