A system and method for aligning the position of a target within a body of a patient to a predetermined position used in the development of a radiation treatment plan can include an ultrasound probe used for generating live ultrasound images, a position sensing system for indicating the position of the ultrasound probe with respect to the radiation therapy device, and a computer system. The computer system is used to display the live ultrasound images of a target in association with representations of the radiation treatment plan, to align the displayed representations of the radiation treatment plan with the displayed live ultrasound images, to capture and store at least two two-dimensional ultrasound images of the target overlaid with the aligned representations of the treatment plan data, and to determine the difference between the location of the target in the ultrasound images and the location of the target in the representations of the radiation treatment plan.