The study of hemodynamic conditions in patient-specific geometries is of great interest to the understanding of cardio-vascular pathologies. Performing large-scale studies of these blood flow conditions requires the building of databases with numerous flow simulations in known correspondences. We propose a method for efficient preparation of the imaging data for use in such studies, comprising an automatic high quality mesh generation strategy and a coordinate mapping technique. Our approach deforms a high quality template mesh to fit a patientspecific geometry using a transformation obtained in a registration step. A valuable feature of this technique is that all the generated meshes are by definition co-registered and have the same mesh topology. This, combined with the coordinate mapping makes direct inter-patient comparisons significantly easier. We apply our method to generate patient-specific meshes of the adbominal aortic bifurcation and demonstrate that it is able to provide high quality meshes in a fully automatic way.