A software pipeline solution to help provide higher accuracy for the targeted bladder cancer treatment external beam radiotherapy (EBRT). This software pipeline can create 3D reconstructions of a bladder or inner surface of an organ using 2D images collected from a flexible cystoscope. Through the use of computer vision image preprocessing techniques and machine learning algorithms scale invariant feature transform (SIFT) and structure from motion (SFM) to identify key points and spatially stich them for reconstruction.