This paper presents the process of digital data flow in RE/CAD/RP/CAI systems to develop models for planning surgical procedures in the craniofacial area. At the first RE modeling stage, digital data processing, segmentation, and the reconstruction of the geometry of the anatomical structures were performed. During the CAD modeling stage, three different concepts were utilized. The first concept was used to create a tool that could mold the geometry of the cranial vault. The second concept was created to prepare a prototype implant that would complement the anterior part of the mandibular geometry. And finally, the third concept was used to design a customized prototype surgical plate that would match the mandibular geometry accurately. Physical models were made using a rapid prototyping technique. A Bambu Lab X1 3D printer was used for this purpose. The process of geometric accuracy evaluation was carried out on manufactured prototypes of surgical plates made of ABS+, CPE, PLA+, and PETG material. In the geometric accuracy evaluation process, the smallest deviation values were obtained for the ABS plus material, within a tolerance of ±0.1 mm, and the largest were obtained for CPE (±0.2 mm) and PLA plus (±0.18 mm). In terms of the surface roughness evaluation, the highest value of the Sa parameter was obtained for the PLA plus material, which was 4.15 µm, and the lowest was obtained for the CPE material, equal to 3.62 µm. The knowledge of the flow of digital data and the identification of factors determining the accuracy of mapping the geometry of anatomical structures allowed for the development of a procedure that improves the modeling and manufacturing of anatomical structures within the craniofacial region.