Apparatus and method for compensating for respiratory and patient motion during treatment

An apparatus and method for performing treatment on an internal target region while compensating for breathing and other motion of the patient is provided in which the apparatus comprises a first imaging device for periodically generating positional data about the internal target region and a second imaging device for continuously generating positional data about one or more external markers attached to the patient's body or any external sensor such as a device for measuring air flow. The apparatus further comprises a processor that receives the positional data about the internal target region and the external markers in order to generate a correspondence between the position of the internal target region and the external markers and a treatment device that directs the treatment towards the position of the target region of the patient based on the positional data of the external markers.