The invention provides methods and apparatus for navigating a medical instrument to a target in the lung. In one embodiment, the invention includes inserting a bronchoscope into the lung, inserting a catheter into the lung through the working channel of the bronchoscope, inserting a tracked navigation instrument wire into the lung through the catheter, navigating the tracked navigation instrument through the lung to the target, advancing the catheter over the tracked navigation instrument to the target, removing the tracked navigation instrument from the catheter, and inserting a medical instrument into the catheter, thus bringing the medical instrument in proximity to the target.