Three-dimensional (3D) reconstructed computed tomography (CT) imaging has become an integral component of craniomaxillofacial patient care. However, with increasing concern regarding the use of ionizing radiation, particularly in children with benign conditions who require repeated examinations, dose reduction and nonionizing alternatives are actively being sought. The “Black Bone” magnetic resonance imaging (MRI) technique provides uniform contrast of the soft tissues to enhance the definition of cortical bone. The aim of this study was to develop methods of 3D rendering of the craniofacial skeleton and to ascertain their accuracy. “Black Bone” MRI datasets acquired from phantoms, adult volunteers and patients were segmented and surface and/or volume rendered using 4 commercially available or open source software packages. Accuracy was explored using a custom phantom (permitting direct measurement), CT and MRI. “Black Bone” MRI datasets were successfully used to create 3D rendered images of the craniofacial skeleton in all 4 software packages. Comparable accuracy was achieved between CT and MRI 3D rendered images of the phantom. The “Black Bone” MRI technique provides a viable 3D alternative to CT examination when imaging the craniofacial skeleton.