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Point-wise Fourier filtering with discrete filter-multiplier is widely used in applications to optical image processing. We propose more general matrix Fourier filtering procedure that permit linear mixing of Fourier modes. The efficiency of matrix Fourier filtering is demonstrated for the problem of controlled pattern formation in feedback optical system under Andronov-Hopf bifurcation conditions. We show that matrix Fourier filtering gives one a powerful tool to construct the spatial shape of eigenfunctions of differential operators and spatial structure of rotating waves.