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In this paper, we study nanostructure-covered laser induced periodic surface structures (NC-LIPSSs) on metals produced by femtosecond laser pulses incident at various angles. For the first time, we show that the dependence of NC-LIPSS period on the incident beam angle deviates significantly from that of regular LIPSSs studied previously using longer laser pulses. Our study shows that this deviation is due to the nanostructures on LIPSSs that can be explained by the Maxwell–Garnett theory of effective media.