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During a crown generation procedure, dental technicians depend on commercial software to generate a margin line to define the design boundary for the crown. The margin line generation remains a non-reproducible, inconsistent, and challenging procedure. In this work, we propose to generate margin line points on prepared teeth meshes using adaptive point learning inspired by the AdaPointTr model. We extracted ground truth margin lines as point clouds from the prepared teeth and crown bottom meshes. The chamfer distance (CD) and infoCD loss functions were used for training a supervised deep learning model that outputs a margin line as a point cloud. To enhance the generation results, the deep learning model was trained based on three different resolutions of the target margin lines, which were used to back-propagate the losses. Five folds were trained and an ensemble model was constructed. The training and test sets contained 913 and 134 samples, respectively, covering all teeth positions. Intraoral scanning was used to collect all samples. Our post-processing involves removing outlier points based on local point density and principal component analysis (PCA) followed by a spline prediction. Comparing our final spline predictions with the ground truth margin line using CD, we achieved a median distance of 0.137 mm. The median Hausdorff distance was 0.242 mm. We also propose a novel confidence metric for uncertainty quantification of generated margin lines during deployment. The metric was defined based on the percentage of removed outliers during the post-processing stage. The proposed end-to-end framework helps dental professionals in generating and evaluating margin lines consistently. The findings underscore the potential of deep learning to revolutionize the detection and extraction of 3D landmarks, offering personalized and robust methods to meet the increasing demands for precision and efficiency in the medical field.