A method and system for extracting a silhouette of a 3D mesh representing an anatomical structure is disclosed. The 3D mesh is projected to two dimensions. Silhouette candidate edges are generated in the projected mesh by pruning edges and mesh points based on topology analysis of the projected mesh. Each silhouette candidate edge that intersects with another edge in the projected mesh is split into two silhouette candidate edges. The silhouette is extracted using an edge following process on the silhouette candidate edges.