The system and method for super resolution processing at long standoff distances in real-time. The system collects a series of image frames and estimated the shift, rotation, and zoom parameters between each of the image frames. A matrix is generated and then an inversion is applied to the matrix to produce a super resolution image of an area of interest while mitigating the effect of any bad pixels on image quality. In some cases, the area of interest is user-defined and in some cases image chips are provided by tracking software. A fast steering mirror can be used to steer and/or dither the focal plane array.