Certain embodiments of the present invention provide a method and system for improved registration of image and navigation references used in image-guided operations. Certain embodiments of the system include an image acquisition device for obtaining at least one image of an object, a first calibration fixture positioned in relation to the image acquisition device, and a second calibration fixture positioned in relation to the object. The position data from first calibration fixture is used to form a characterization of the image acquisition device, which is corrected by position data from the second calibration fixture. In an embodiment, a first calibration fixture is affixed to a C-arm camera and a smaller second calibration fixture is affixed to a patient. Data from the first and second calibration fixtures is used with tracking data to calibrate the image acquisition data and register reference points in image and navigation reference frames.