Methods and systems for navigating to a target through a patient's bronchial tree are disclosed including a bronchoscope, a probe insertable into a working channel of the bronchoscope including a location sensor, and a workstation in operative communication with the probe and the bronchoscope the workstation including a user interface that guides a user through a navigation plan and is configured to present a three-dimensional (3D) view for displaying a 3D rendering of the patient's airways and a corresponding navigation plan, a local view for assisting the user in navigating the probe through peripheral airways of the patient's bronchial tree to the target, and a target alignment view for assisting the user in aligning a distal tip of the probe with the target.