Cone beam computed tomography (CBCT) has emerged as a crucial radiographic technique for orthodontic diagnosis and treatment planning, particularly for cases requiring the assessment of complex anatomical relationships. In the first part of the study, we examined metric characteristics measured on 3D cranial models of patients before and after surgery. In the second part, we conducted more complex data processing, analyzing a set of 12 cranial feature points using Procrustes analysis to quantify and visually represent surgical modifications. The third part involved comparing 3D facial surfaces using Iterative Closest Point (ICP) alignment and nearest point-to-point distances. Additionally, we tested point configurations in the facial soft tissues. The study included a group of orthodontic patients from whom CBCT data and 3D facial scans were obtained during treatment. The results demonstrated that each method could assess preoperative and postoperative changes to varying degrees. They also highlighted potential gender differences in surgical modifications that warrant further investigation and consideration during surgical planning. The aim of our study was to compare 3D visualizations of skull and facial models before and after surgery, to assess the degree of relative agreement or similarity, and to identify any morphological differences.