A method and system is presented for treating moving target regions in a patient's anatomy by creating radiosurgical lesions. The method includes determining a pulsating motion of a patient separately from a determining of a respiratory motion, and directing a radiosurgical beam, from a radiosurgical beam source, to a target in the patient based on the determining of the pulsating motion. Directing the radiosurgical beam to the target may include creating a lesion in the heart to inhibit atrial fibrillation. The method may further include determining the respiratory motion of the patient, and compensating for movement of the target, due to the respiratory motion and the pulsating motion of the patient, in the directing of the radiosurgical beam based on the determining of the respiratory motion and the determining of the pulsating motion.