Patients with Apert syndrome experience midfacial hypoplasia, hypertelorism, and downslanting palpebral fissures which can be corrected by midfacial bipartition distraction with rigid external distraction device. Quantitative studies typically focus on quantifying rigid advancement and rotation postdistraction, but intrinsic shape changes of bone and soft tissue remain unknown. This study presents a method to quantify these changes. Pre-and post-operative computed tomography scans from patients with Apert syndrome undergoing midfacial bipartition distraction with rigid external distraction device were collected. Digital Imaging and Communications in Medicine files were converted to three-dimensional bone and soft tissue reconstructions. Postoperative reconstructions were aligned on the preoperative maxilla, followed by nonrigid iterative closest point transformation to determine local shape changes. Anatomical point-to-point displacements were calculated and visualized using a heatmap and arrow map. Nine patients were included.