The present 3D dataset contains 15 specimens selected from the 69 3D models analyzed in the paper “3D topography as an indicator of change in food processing ability in the conodont genus Palmatolepis elements”. 3D topographic analysis of Palmatolepis P1 conodont elements from the Late Devonian period revealed an increase in blade sharpness together with a reduction in platform size. This indicates morphofunctional adaptation to more efficient prey processing.