Current surgical treatment planning systems predict three-dimensional (3D) corrections from two-dimensional (2D) data and are inadequate for complex movements. In this paper, we present a 3D planning system based on computed tomographic (CT) data. A three-dimensional CT scan of the craniofacial skeleton forms the database. Software developed in the Harvard Surgical Planning Laboratory was modified for the craniofacial skeleton. Reproducible skeletal landmarks are identified for superimposition. A 'cutting tool' is used to segment the mandible and segments are moved to their predicted positions. A 'collision tool', alerts the operator of skeletal interferences. An analysis of selected scans is used to demonstrate the system. Three-dimensional visualization of the facial skeleton, selection of landmarks, measurement of angles and distances, simulation of osteotomies, repositioning of bones, detection of collisions and super-imposition of scans were accomplished. In an illustrative case of Hemifacial Microsomia, predicted and actual 3D corrective movements of the entire mandible were documented. Analysis of scans indicated that 3D planning can prevent insufficient jaw lengthening or other surgical inaccuracies which occur with standard 2D methods. Software demonstrated here will allow the surgeon to accurately plan treatment and evaluate craniomaxillofacial surgery outcomes. Future applications may include surgical navigation.