A method and apparatus for presenting three-dimensional data to a physician is provided to facilitate the flexible navigation of an endoscope and surgical instruments with respect to anatomical structures. In accordance with a first embodiment a first set of data corresponding to a three dimensional model of a patients anatomy is received. This three-dimensional model may be rendered from images taken in CT or MRI scanning, as discussed above. In accordance with this embodiment, this model is then combined with a second set of data corresponding to a view obtained from an endoscope. In another embodiment, the view from the illustrative endoscope is displayed as an inset image on the display of the three-dimensional image. In yet another embodiment, the three-dimensional image comprises a graphical representation of at least a first surgical instrument, such as said endoscope. The surgeon may select among various combinations of views and may zoom in or out from any particular view.
