A method and system for treating tissue with a surgical device includes the steps of displaying an image created by collecting imaging data from an imaging device, selecting at least one tissue target from the image, collecting image data and tracking the tissue target during at least one respiration cycle, determining the dwell position of the tissue target, and displaying an image created from image data collected with the tissue target at the dwell position. The method may further include determining the position and orientation of the surgical device with respect to the dwell position and indicating the trajectory of the surgical device on the display screen. The method may further include the steps of monitoring the respiration cycle, indicating when the tissue target is approaching the dwell position, positioning the surgical device in the patient based upon the dwell position and trajectory and treating the tissue target.