Methods and systems for three-dimensional (3D) reconstruction of endoscopic data in accordance with embodiments of the invention are described. In one embodiment, a method for processing a plurality of images captured by an endoscope includes preprocessing a plurality of images captured by an endoscope and including at least a portion of an organ. In many embodiments of the invention, the preprocessing includes estimating variations in light intensity within scenes captured by the plurality of images, and generating a set of color-adjusted images based on those variations. The method according to some embodiments of the invention may include generating a 3D point cloud representing points on a surface of the organ based on the set of color-adjusted images, defining a mesh representing the surface of the organ based on the 3D point cloud, and generating a texture of the surface of the organ based on the set of color-adjusted images.