Dental crowns are essential dental treatments for restoring damaged or missing teeth of patients. Recent design approaches of dental crowns are carried out using commercial dental design software. Once a scan of a preparation is uploaded to the software, a dental technician needs to manually define a precise margin line on the preparation surface, which constitutes a non-repeatable and inconsistent procedure. This work proposes a new framework to determine margin lines automatically and accurately using deep learning. A dataset of incisor teeth was provided by a collaborating dental laboratory to train a deep learning segmentation model. A mesh-based neural network was modified by changing its input channels and used to segment the prepared tooth into two regions such that the margin line is contained within the boundary faces separating the two regions. Next, k-fold cross-validation was used to train 5 models, and a voting classifier technique was used to combine their results to enhance the segmentation. After that, boundary smoothing and optimization using the graph cut method were applied to refine the segmentation results. Then, boundary faces separating the two regions were selected to represent the margin line faces. A spline was approximated to best fit the centers of the boundary faces to predict the margin line. Our results show that an ensemble model combined with maximum probability predicted the highest number of successful test cases (7 out of 13) based on a maximum distance threshold of 200 m (representing human error) between the predicted and ground truth point clouds. It was also demonstrated that the better the quality of the preparation, the smaller the divergence between the predicted and ground truth margin lines (Spearman's rank correlation coefficient of -0.683). We provide the train and test datasets for the community.