Methods for generating a centerline or skeleton structure within a 3D virtual object are provided. A first method defines a centerline based on distance from boundary values along points of the defined centerline. A second method uses a distance from boundary field to assign costs to voxels in the virtual object and defines a minimum cost spanning tree based on assigned costs. The centerline is defined along the minimum cost spanning tree. Branches along the centerline are identified and added to the centerline to define a skeleton.