A method and system for determining a target location for a medical device having complex geometry relative to an anatomical feature, and for navigating and positioning the medical device at the target location. The system may include a medical device including a treatment element having a centroid, one or more navigation electrodes, and a longitudinal axis and a navigation system in communication with the one or more navigation electrodes, the navigation system including a processing unit. The processing unit may be programmed to define a plane that approximates a surface of the anatomical feature, define a centroid of the anatomical feature, define a vector that is normal to the plane and extends away from the centroid of the anatomical feature, and determine a target location for the treatment element of the medical device based on the vector to assist the user in placing the device for treatment.