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The choice of technique for the creation of a 3D digital human bone model from natural specimens has a critical impact on the final result and usability of the obtained model. The cornerstone factor in 3D modeling is the number of faces of polygon mesh, along with topological accuracy, as well as resolution and level of detail of the texture map. Three different techniques (3D scanning, photogrammetry, and micro-computed tomography) have been used to create a digital 3D model of the human zygomatic bone. As implementation and use of 3D models can be divided into three main categories—visualization, simulation, and physical replication to obtain a functioning model (implant or prothesis)—the obtained models have been evaluated by the density and topological accuracy of the polygonal mesh, as well as by visual appearance by inspecting the obtained texture map. The obtained data indicate that for biomedical applications and computer biomechanical simulation the most appropriate technique of 3D model obtainment is micro-computed tomography, in its turn for visualization and educational purposes, the photogrammetry technique is a more preferable choice.