A method and apparatus for deep learning based automatic bone removal in medical images, such as computed tomography angiography (CTA) volumes, is disclosed. Bone structures are segmented in a 3D medical image of a patient by classifying voxels of the 3D medical image as bone or non-bone voxels using a deep neural network trained for bone segmentation. A 3D visualization of non-bone structures in the 3D medical image is generated by removing voxels classified as bone voxels from a 3D visualization of the 3D medical image.