To compare the accuracy of linear and angular measurements between cephalometric and anatomic landmarks on surface models derived from 3D cone beam computed tomography (CBCT) with two different segmentation protocols was the aim of this study. CBCT scans were made of cadaver heads and 3D surface models were created of the mandible using two different segmentation protocols. A high-resolution laser surface scanner was used to make a 3D model of the macerated mandibles. Twenty linear measurements at 15 anatomic and cephalometric landmarks between the laser surface scan and the 3D models generated from the two segmentation protocols (commercial segmentation (CS) and doctor's segmentation (DS) groups) were measured. The interobserver agreement for all the measurements of the all three techniques was excellent (intraclass correlation coefficient 0.97-1.00). The results are for both groups very accurate, but only for the measurements on the condyle and lingual part of the mandible, the measurements in the CS group is slightly more accurate than the DS group. 3D surface models produced by CBCT are very accurate but slightly inferior to reality when threshold-based methods are used. Differences in the segmentation process resulted in significant clinical differences between the measurements. Care has to be taken when drawing conclusions from measurements and comparisons made from different segmentations, especially at the condylar region and the lingual side of the mandible.