The present invention provides a method for real-time tracking of moving flexible surfaces and an image guided surgical robotic system using this tracking method. A vision system acquires an image of the moving flexible surface and identifies and tracks visual features at different times. The method involves computing both rigid and stretching transformations based on the changing positions of the visual features which are then used to track any area of interest on the moving flexible surface as it evolves over time. A robotic surgical system using this real-time tracking is disclosed.