Three-dimensional (3D) computer-assisted planning requires detailed visualisation of the craniomaxillofacial region and interocclusal relationship. The aim of this study was to establish and evaluate a method to create a 3D model of the craniomaxillofacial region and to adopt intraoral digital scanning to place the lower jaw into a centric relation (CR) without the need of additional plaster casts and model surgery. A standard plastic skull modified by metallic dental wires and brackets was subjected to computed tomography (CT), cone beam computed tomography (CBCT), and intraoral digital scanning. We evaluated two different virtual bite registrations, a digital scan of the buccal dental surfaces and scanning of the wax bites to position the lower jaw into a CR, and assessed the accuracy of the integration of intraoral scanning to the CT/CBCT scans. The mean registration error of corresponding mesh points for the CT and intraoral scanned images was 0.15 ± 0.12 mm, while this error was 0.18 ± 0.13 mm for the CBCT and intraoral scanned images. The mean accuracy of the two virtual bite registrations ranged from 0.41 to 0.49 mm (buccal scan technique) and from 0.65 to 1.3 mm (virtualised wax bite technique). A method for virtual bite registration was developed. It has the potential to eliminate plaster casts and model surgery and may facilitate 3D computer-assisted planning of orthognathic surgery cases.