1. A method of a digital processor for estimating stereo misalignment using modified affine or perspective model, comprising: 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.