Methods and systems for processing and/or superimposing a medical image of an anatomical body (e.g., a heart) with graphical information are provided. Reference elements and/or reference catheter are placed in contact with the anatomical body. A physical structure within a navigational coordinate system is located using the reference elements and/or reference catheter. An image reference within an image coordinate corresponding to the physical structure is located. Location of the image reference can be accomplished, e.g., by displaying the medical image and electronically marking the displayed image reference, or by automatically locating image data corresponding to the image reference. The navigational and image coordinate systems are then registered based on the location of the physical structure within the navigational coordinate system and the location of the image reference within the image coordinate system, which allows graphical information to be accurately merged with the medical image data.