The study aim is to investigate the influence of scan field, mouth opening, voxel size, and segmentation threshold selections on the quality of the three-dimensional (3D) surface models of the dental arches from cone beam computed tomography (CBCT). 3D models of 25 patients scanned with one image intensifier CBCT system (NewTom 3G, QR SLR, Verona, Italy) using three field sizes in open- and closed-mouth positions were created at different voxel size resolutions. Two observers assessed the quality of the models independently on a five-point scale using specified criteria. The results indicate that large-field selection reduced the visibility of the teeth and the interproximal space. Also, large voxel size reduced the visibility of the occlusal surfaces and bone in the anterior region in both maxilla and mandible. Segmentation threshold was more variable in the maxilla than in the mandible. Closed-mouth scan complicated separating the jaws and reduced teeth surfaces visibility. The preliminary results from this image-intensifier system indicate that the use of medium or small scan fields in an open-mouth position with a small voxel is recommended to optimize quality of the 3D surface model reconstructions of the dental arches from CBCT. More research is needed to validate the results with other flat-panel detector-based CBCT systems.