A method and apparatus for estimating stereo misalignment using modified affine or perspective model. The method includes dividing a left frame and a right frame into blocks, comparing horizontal and vertical boundary signals in the left frame and the right frame, estimating the horizontal and the vertical motion vector for each block in a reference frame, selecting a reliable motion vectors from a set of motion vectors, dividing the selected block into smaller features, feeding the data to an affine or a perspective transformation model to solve for the model parameters, running the model parameters through a temporal filter, portioning the estimated misalignment parameters between the left frame and right frame, and modifying the left frame and the right frame to save some boundary space.