The Gannochy Trust innovation award of the Royal Society of Edinburgh (RSE) will be given to Dr. Colin Urquhart, of Glasgow-based Dimensional Imaging on November 7.
The system can help scientists make life-like facial models of the patients, both before and after surgery.
The technology could enable clinicians to simulate what the results of surgery may look like.
The system is already in use worldwide mainly in the field of facial surgery.
Urquhart said that he was "very honoured".
"Scotland is an excellent place for Dimensional Imaging to be based as it allows us to access the critical mass of world-leading expertise in imaging processing and computer vision in Scotland's universities," the BBC quoted Urquhart as saying.
He added: "This award is a tremendous encouragement to me and my colleagues, whose dedication, team work and constant innovation is invaluable."
Urquhart has also won a 50,000 pounds prize and a specially commissioned gold medal.
RSE president Lord Wilson of Tillyorn, said: "Dr Urquhart's innovation has the potential to make a real and lasting difference to the lives of a great many people.
"The precision and high definition of this Dimensional Imaging technology offers scope for a large range of uses. Our panel of judges, chaired by Lord Cullen, were greatly impressed.
"I am delighted that, as a result of the Gannochy Trust's generous support, we are able to recognise Dr Urquhart's achievement."
Also, the new technology has many implications in orthodontics, psychology and in the entertainment games and film industry.