This disclosure involves generating and outputting a segmentation model using 3D models having user-provided labels and scene graphs. For example, a system uses a neural network learned from the user-provided labels to transform feature vectors, which represent component shapes of the 3D models, into transformed feature vectors identifying points in a feature space. The system identifies component-shape groups from clusters of the points in the feature space. The system determines, from the scene graphs, parent-child relationships for the component-shape groups. The system generates a segmentation hierarchy with nodes corresponding to the component-shape groups and links corresponding to the parent-child relationships. The system trains a point classifier to assign feature points, which are sampled from an input 3D shape, to nodes of the segmentation hierarchy, and thereby segment the input 3D shape into component shapes.