Craniometaphyseal dysplasia is an extremely rare, genetic bone-remodeling disorder. Comparable to osteopetrosis, fibrous dysplasia, and other infrequent conditions, craniometaphyseal dysplasia is characterized by progressive diffuse hyperostosis of the neuro- and viscerocranium. Affected patients present with a pathognomonic dysmorphia: macrocephalus, hypertelorism, bulky facial skeleton, and a prominent mandible. Progressive thickening and petrification of the craniofacial bones can continue throughout life, often resulting in neurological symptoms due to obstruction of the cranial nerves in the foramina and therefore immediately requiring neurosurgical interventions to avoid persistent symptoms with severe impairment of function. Treatment is largely infeasible given the lack of suitable tools to perform a craniotomy through the gross calvarial bone. In this paper, the authors present a complete process chain from the CT-based generation of an individual patient's model displaying his pathology to optimized preoperative planning of the skull's shape with a thickness of about 6-7 mm. For concise verification of the surgical plan in an operating room environment, a 3D real-time navigation prototype system was utilized. To guarantee realization of the surgery in a reasonable time frame, the mechanical tools were preoperatively selected for optimizing the ablation rate in porcine and bovine bone, which were comparable to that in the patient. This process chain was developed in a modular way, so that it could be easily adopted completely or partially for other surgical indications. A 21-year-old man was treated according to this sophisticated concept. Skull bone more than 50 mm thick in some regions was reduced to physiological thickness. The patient was thus in a stage that neurosurgical interventions could be performed with a regular risk within a reasonable time of treatment.