A method and system for automatic multi-organ segmentation in a 3D image, such as a 3D computed tomography (CT) volume using learning-base segmentation and level set optimization is disclosed. A plurality of meshes are segmented in a 3D medical image, each mesh corresponding to one of a plurality of organs. A level set in initialized by converting each of the plurality of meshes to a respective signed distance map. The level set optimized by refining the signed distance map corresponding to each one of the plurality of organs to minimize an energy function.