Accurately and quantitatively investigating morphological variation in fossil assemblages requires appropriate analytical methods. Through the use of imaging techniques, 3D digital twins of existing objects have opened up the possibility of developing innovative protocols for in silico analyses of variation patterns in fossil primate bones and teeth. Landmark-based geometric morphometrics initiated a critical methodological shift in the discipline, leading to significant discoveries in palaeontology. However, in some cases (e.g., smooth and complex structures, discrete traits) landmark-based geometric morphometrics fail to fully capture differences in shape.