Recent progress in imaging and image processing techniques has provided for improvements in odontological research in a variety of aspects. Thus, the presented method has been developed precisely in order to assess metrically 3D reconstructions of teeth. Rapidly and accurately obtained data of a wide range and appropriate density are sufficient enough for morphometric studies rather than tooth size assessments which are inherent to conventional techniques. The main contributions providing for holistic and objective morphometric analysis of teeth are the following: (1) interpretation of basic dental morphological features; (2) automated of orientational coordinate system setup based on tooth surface analysis; (3) new tooth morphometric parameters which could not be obtained through application of conventional odontometric techniques; (4) methodological novelty for automated odontomorphometric analysis pipeline. Application of tomographic imaging, which has been used for obtaining 3D models, expands the proposed method potential further through providing detailed and comprehensive reconstructions of teeth. The current study was conducted on unique material from the archaeological site of Sunghir related to the Upper Palaeolithic period. Metric assessments of external and internal morphological layers of teeth were performed in common orientation and sectioning. The proposed technique allowed more profound analysis of Sunghirian teeth which date back to the times of modern human morphology formation.