A complex three dimensional network structure results when blood fibrin polymerizes into branching threads. To understand the rheological behavior of fibrin clots and how this behavior is associated with network morphology, one must obtain quantitative measurements of morphometric parameters of the networks (e.g., fiber diameter, distance between branching points of fibers, and branching complexity) formed under various conditions. Over the past several years, researchers have measured the parameters manually from the 3D reconstruction of networks using stereo images generated with intermediate voltage electron microscopy. Our goal is to help automate this time consuming process as much as possible, and skeletonization is a promising tool. Skeletonization is a process of transforming an object into idealized thin lines. Although various techniques for skeleton computation have been developed, most of them require explicit boundary information of the objects being skeletonized, which is not directly available from raw images.