1. Method for registering a three dimensional (3D) coordinate system with a Medical Positioning System (MPS) coordinate system, and with a two dimensional (2D) coordinate system, the method comprising the procedure of: acquiring at least one 2D image of a volume of interest, said volume of interest including at least one organ within the body of a patient, said 2D image being associated with said 2D coordinate system; acquiring a plurality of MPS points within said at least one 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 at least one organ from at least one pre-acquired 3D image of said volume of interest, said at least one pre-acquired 3D image and said 3D image model being associated with said 3D coordinate system; estimating a volumetric model of said at least one organ according to said at least one 2D image and said acquired MPS points; and registering said 3D coordinate system with said MPS coordinate system and with said 2D 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.