The present disclosure relates to a method and apparatus to improve model-based organ segmentation with image post-processing using one or more processors. The method includes: receiving three-dimensional (3D) CT or MR images and the corresponding voxel-by-voxel segmentation results from the output of an automatic DCNN segmentation model, analyzing the segmentation results on a 3D basis according to organ anatomical information, processing the results to identify regions with anatomically incorrect segmentations, fixing the incorrect segmentations, analyzing the remaining segmentation results on a two-dimensional (2D) and slice-by-slice basis according to predefined organ segmentation criteria, identifying the start and end slices, processing the results to remove segmentations beyond the identified slices to obtain the final results.