A system for planning routes through an organ, comprising a lumen and at least one region of interest, comprising: a memory for storing information about the organ and an endoscopic procedure associated with the organ, wherein the information includes: anatomical constraints that define locations or organs to avoid; anatomical constraints that confine the route within specific geometric locations; a metric for selecting the most appropriate route; the definition of the ROI; a segmentation of the organ through which navigation will occur in either the 3D image or in the real organ with an endoscopic device, the central axes of the segmented organ; and a parametric description of the endoscopic device; and a processor operative to perform the following functions: a) access the stored information and automatically determine at least one route destination along said lumen and in close proximity to the ROI, and to automatically determine at least one complete route through the organ from a base of the organ to the route destination based on at least each of anatomical, endoscopic-device, and procedure-specific constraints, and b) sending information to a display device causing the route to be displayed on the display device in conjunction with a three-dimensional image of the organ; wherein the ROI is outside of the lumen, and the processor is further operative to determine a route extension from the lumen to the ROI. a memory for storing information about the organ and an endoscopic procedure associated with the organ, wherein the information includes: anatomical constraints that define locations or organs to avoid; anatomical constraints that confine the route within specific geometric locations; a metric for selecting the most appropriate route; the definition of the ROI; a segmentation of the organ through which navigation will occur in either the 3D image or in the real organ with an endoscopic device, the central axes of the segmented organ; and a parametric description of the endoscopic device; and a processor operative to perform the following functions: a) access the stored information and automatically determine at least one route destination along said lumen and in close proximity to the ROI, and to automatically determine at least one complete route through the organ from a base of the organ to the route destination based on at least each of anatomical, endoscopic-device, and procedure-specific constraints, and b) sending information to a display device causing the route to be displayed on the display device in conjunction with a three-dimensional image of the organ; a) access the stored information and automatically determine at least one route destination along said lumen and in close proximity to the ROI, and to automatically determine at least one complete route through the organ from a base of the organ to the route destination based on at least each of anatomical, endoscopic-device, and procedure-specific constraints, and b) sending information to a display device causing the route to be displayed on the display device in conjunction with a three-dimensional image of the organ; wherein the ROI is outside of the lumen, and the processor is further operative to determine a route extension from the lumen to the ROI.