Abstract Purpose The purpose of this paper is to present and validate a new semi-automated 3D surface mesh segmentation approach that optimizes the laborious individual human vertebrae separation in the spinal virtual surgical planning workflow and make a direct accuracy and segmentation time comparison with current standard segmentation method. Methods The proposed semi-automatic method uses the 3D bone surface derived from CT image data for seed point-based 3D mesh partitioning. The accuracy of the proposed method was evaluated on a representative patient dataset. In addition, the influence of the number of used seed points was studied. The investigators analyzed whether there was a reduction in segmentation time when compared to manual segmentation. Surface-to-surface accuracy measurements were applied to assess the concordance with the manual segmentation. Results The results demonstrated a statically significant reduction in segmentation time, while maintaining a high accuracy compared to the manual segmentation. A considerably smaller error was found when increasing the number of seed points. Anatomical regions that include articulating areas tend to show the highest errors, while the posterior laminar surface yielded an almost negligible error. Conclusion A novel seed point initiated surface based segmentation method for the laborious individual human vertebrae separation was presented. This proof-of-principle study demonstrated the accuracy of the proposed method on a clinical CT image dataset and its feasibility for spinal virtual surgical planning applications.