1. A method for characterizing spatial distortion of a medical imaging system, the method comprising: estimating a contour and dimensions of a desired target volume; determining a desired coordinate system; determining a desired arrangement and spacing of a plurality of control points, wherein the desired arrangement and spacing is matched to the determined contour, dimensions, and coordinate system; fabricating a three dimensional phantom matched to the determined arrangement and spacing of the plurality of control points and configured to define the control points in a substantially rigid structure; fixing the phantom with respect to a stereotactic frame such that the plurality of control points defines a corresponding plurality of first known spatial locations; imaging the phantom; determining second measured spatial locations based on the imaging; comparing at least a selected subset of the first known spatial locations with corresponding second measured spatial locations; and calculating indicia of any indicated spatial distortion between the first known spatial locations and the corresponding second measured spatial locations.