1. Method for registering a three dimensional (3D) coordinate system with a Medical Positioning System (MPS) coordinate system and a two dimensional (2D) coordinate system, the method comprising: acquiring a 2D image of a volume of interest, said volume of interest including an organ within the body of a patient, said 2D image being associated with said 2D coordinate system; acquiring MPS points within said organ, said MPS points being associated with said MPS coordinate system, said MPS coordinate system being registered with said 2D coordinate system; extracting a 3D image model of said organ from a pre acquired 3D image of said volume of interest, said pre acquired 3D image and said 3D image model being associated with said 3D coordinate system; estimating a volumetric model of said organ according to said acquired MPS points; and registering said 3D coordinate system with said MPS coordinate system by matching said extracted 3D image model with said estimated volumetric model, wherein said 2D coordinate system, said 3D coordinate system, and said MPS coordinate system are three different coordinate systems.