Methods, systems, and computer readable media for deriving a three-dimensional (3D) textured surface from endoscopic video are disclosed. According to one method for deriving a 3D textured surface from endoscopic video, the method comprises: performing video frame preprocessing to identify a plurality of video frames of an endoscopic video, wherein the video frame preprocessing includes informative frame selection, specularity removal, and key-frame selection; generating, using a neural network or a shape-from-motion-and-shading (SfMS) approach, a 3D textured surface from the plurality of video frames; and optionally registering the 3D textured surface to at least one CT image.