Digital metrologywas applied to evaluate 3D models of the unique skull of a fossil tetrapod, Madygenerpeton pustulatum, generated using various 3D digitization methods. The skull surface is covered by minute tubercles making it challenging for digitization with appropriate accuracy. Uniqueness and fragility of the specimen preclude the use of tactile measuring systems for creating a standardized reference model. To overcome this problem, comparative analysis of the triangulated models generated from the clouds of points obtained with seven different devices was conducted using the Geomagic Studio and Autodesk PowerShape CAD software. In the proposed approach, geometrically and dimensionally closest-fitting models underwent detailed statistical analysis between surface polygons in three steps. First, 3D models obtained from different scanning methods were compared with each other in couples. Next, statistical analysis of the differences between the coupled models was performed. Finally, a rating list of the models related to the required accuracy was prepared. The proposed approach is applicable to any other scanned object, especially in palaeontological applications, where each object is unique and exhibits individual features.