1. A method for automatic registration of multiple measurement modes of a target body, comprising the steps of: receiving first data comprising a first plurality of measured values each associated with a plurality of coordinate values for three spatial dimensions based on a first measurement device for measuring a target body; receiving second data comprising a second plurality of measured values each associated with a plurality of coordinate values for three spatial dimensions based on a different second measurement device for measuring the target body, wherein the first measurement device and the second measurement device are mounted on the same combined apparatus and are mechanically aligned; determining a non-rigid transform between the first data and the second data without human intervention based on the first data and the second data, wherein the non-rigid transform determines changes in the plurality of coordinate values for each of the plurality of measured values of the second data to increase a measure of similarity between a measured value of the first data and a nearby measured value of the second data, which changes are not accounted for by a constant value for a three dimensional translation and a constant value for a three dimensional rotation over the plurality of measured values of the second data; and transforming the plurality of coordinate values for each measured value of the second data based on the non-rigid transform.