A method and system for segmentation and removal of pulmonary arteries, pulmonary veins, and a left atrial appendage from 3D medical image data, such as 3D computed tomography (CT) volumes, is disclosed. A global shape model is segmented for each of pulmonary arteries, pulmonary veins, and a left atrial appendage in a 3D volume. The segmented global shape model for each of the pulmonary arteries, pulmonary veins, and left atrial appendage is locally refined based in local voxel intensities in the 3D volume, resulting in a respective mask for each structure. The mask is used to remove voxels belonging to the pulmonary arteries, pulmonary veins, and left atrial appendage from the 3D volume in order to better visualize coronary arteries and bypass arteries.