This paper describes a set of software tools which we developed for the calculation of fluid flow through cardiovascular organs. Our tools work with medical data from a CT scanner, but could be used with any other 3D input data. For meshing we used a Tetgen tetrahedral mesh generator, as well as a mesh re-generator that we have developed for conversion of tetrahedral elements into bricks. After adequate meshing we used our PAKF solver for calculation of fluid flow. For human-friendly presentation of results we developed a set of post-processing software tools. With modification of 2D mesh (boundary of cardiovascular organ) it is possible to do virtual surgery, so in a case of an aorta with aneurism, which we had received from University Clinical center in Heidelberg from a multi-slice 64-CT scanner, we removed the aneurism and ran calculations on both geometrical models afterwards. The main idea of this methodology is creating a system that could be used in clinics.