A system for tracking an instrument including an intraoperative transducer array configured to generate signals from array positions to generate real-time images of an area of interest. The instrument can be a penetrating instrument having a sensor mounted at a position of interest and being responsive to the signals from the array positions. A signal processing module can be provided and configured to determine a position and orientation of the instrument in accordance with the signals and to classify media of the position of interest based upon a response of the sensor to the signals from the array positions. An overlay module can be provided and configured to generate an overlay image registered to the real-time images to identify a position of the position of interest and provide feedback on the media in which the position of interest is positioned. A display can be provided and configured to provide visual feedback of the overlay image on the real-time images.