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Material processing using a laser has become a widely used method for industrial procedures (e.g. laser welding or cutting). Furthermore the medical laser has become an integral part of dermatology, neurosurgery, ENT, esthetic, plastic and general surgery. Recent publications have shown, that the short pulsed CO2 laser is suitable to ablate bony and cartilage tissue and proposes fundamentally new operative techniques in medicine. The obtainable precision in cutting (in the hundred micrometers range) with a laser system can only be reached using means of computer and robot assisted surgery. We established the first robot assisted laser bone ablation setup, comprising a prototype CO2 laser system and a six degree of freedom robot. The laser beam is guided through a passive articulated mirror arm to the robots end-effector. The end-effector is composed of a two mirror galvanometric scan head, which deflects the pulsed laser beam onto the tissue. In this paper we present an end-effector calibration and registration method to determine the parameters which are critical in obtaining precise and accurate cutting results.