Recent developments in computational modeling of human arteries have opened the possibility of performing subject-specific analyses on increasingly larger numbers of subjects. This achievement will eventually lead to a better understanding of the role of geometry and hemodynamics in the initiation and development of vascular disease. The availability of data from population or longitudinal studies raises the problem of quantitatively comparing distributions of geometric and hemodynamic quantities among different models. This task is made difficult by the fact that modeled arterial segments typically comprise bifurcations and regions of high curvature. A technique for comparing surface distributions among realistic models of the carotid bifurcation has been recently proposed in [1]. In that work, surface mesh nodes were classified as belonging to semi-automatically defined quadrilateral patches, and nodal quantities of interest averaged over each patch. This avoided node-to-node comparison and the need for registration. However, patch definition required user interaction and was thus subject to operator-variability. In this work we present a fully automated technique for parameterization and patching of the surface of bifurcating vessels. The method is based on robust and objective schemes aimed at preserving the consistency of the parameterization over a wide range of bifurcating geometries, allowing quantitative comparison of surface distributions in presence of high anatomic variability.