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a novel adaptable accurate way for calculating Polar FFT and Log-Polar FFT is developed in this paper, named Multilayer Fractional Fourier Transform (MLFFT). MLFFT is a necessary addition to the pseudo-polar FFT for the following reasons: It has lower interpolation errors in both polar and log-polar Fourier transforms; it reaches better accuracy with the nearly same computing complexity as the pseudo-polar FFT; it provides a mechanism to increase the accuracy by increasing the user-defined computing level. This paper demonstrates both MLFFT itself and its advantages theoretically and experimentally. By emphasizing applications of MLFFT in image registration with rotation and scaling, our experiments suggest two major advantages of MLFFT: 1) scaling up to 5 and arbitrary rotation angles, or scales up to 10 without rotation can be recovered by MLFFT while currently the result recovered by the state-of-the-art algorithms is the maximum scaling of 4; 2) No iteration is needed to obtain large rotation and scaling values of images by MLFFT, hence it is more efficient than the pseudopolar-based FFT methods for image registration.