A method for registering a catheter navigation system to a three-dimensional image generally includes obtaining a three-dimensional image including position information for a plurality of surface points on a part of a patient's body, using a catheter navigation system to place a tool at a location on the surface of the patient's body, measuring position information for the surface location, identifying a corresponding location on the image, associating position information for the surface location and the location identified on the image as a fiducial pair, and using at least one fiducial pair to generate a mapping function. The mapping function transforms points within the coordinate system of the catheter navigation to the coordinate system of the three-dimensional image such that, for each fiducial pair, the mapping error is about zero. Suitable warping algorithms include thin plate splines, mean value coordinates, and radial basis function networks.