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We have been numerically demonstrated the mechanism of spatial beam filtering with autocloned photonic crystals. The spatial filtering through different configurations of the multilayered structures based on a harmonically modulated substrate profile is considered. The paper demonstrates a series of parameter studies to look for the best spatial beam filtering performance. The optimization results show that a beam spectral width of 39.2° can be reduced to that of 5.92°, leading to high potential applications for integrated optical microsystems.