Objective: The purpose of this study is to propose a complete methodology for automatically registering three-dimensional (3D) pre-operative and post-operative CT scan dental volumes as well as to provide a toolset for quantifying and evaluating their volumetric differences. Methods: The proposed methodology was applied to cone beam CT (CBCT) data from 20 patients in order to assess the volume of augmented bone in the alveolar region. In each case, the pre-operative and post-operative data were registered using a 3D affine-based scheme. The performance of the 3D registration algorithm was evaluated by measuring the average distance between the edges of the registered sets. The differences between the registered sets were assessed through 3D subtraction radiography. The volume of the differences was finally evaluated by defining regions of interest in each slice of the subtracted 3D data and by combining all respective slices to model the desired volume of interest. The effectiveness of the algorithm was verified by applying it to several reference standard-shaped objects with known volumes. Results: Satisfactory alignment was achieved as a low average offset of 1.483 ± 1.558 mm was recorded between the edges of the registered sets. Moreover, the estimated volumes closely matched the volumes of the reference objects used for verification, as the recorded volume differences were less than 0.4 mm3 in all cases. Conclusion: The proposed method allows for automatic registration of 3D CBCT data sets and the volumetric assessment of their differences in particular areas of interest. The proposed approach provides accurate volumetric measurements in three dimensions, requiring minimal user interaction.