Systems and methods are described for automating aspects of minimally invasive therapeutic treatment of patients. In one embodiment a robotic catheter system may comprise a controller including a master input device; and an electromechanically steerable elongate instrument having a proximal interface portion and a distal portion, the proximal interface portion being configured to be operatively coupled to an electromechanical instrument driver in communication with the controller, the distal portion being configured to be interactively navigated adjacent internal tissue structures of a patient's body in response to signals from the controller; wherein the distal portion of the elongate instrument comprises an antenna operatively coupled to the controller, and wherein the controller is configured to determine the temperature of structures adjacent to the distal portion of the elongate instrument utilizing radiometry analysis.