Based on the rigorous couple-wave analysis (RCWA) method, columned ZnSe sub-wavelength micro-structure by genetic algorithm (GA) is optimized and optimum structure parameters are obtained. The effect of structure parameter error and profile shape error of columned ZnSe structure on the anti-reflective properties in actual manufacturing process is discussed. The transmittance of the multilevel ZnSe gratings with coned profile is also presented as a function of the structure height. The results show that the columned ZnSe micro-structure can have excellent average anti-reflective properties between 8 μm and 14 μm at normal incidence when the structure period, height and filling factor are 3.3 μm, 1.7517 μm and 0.7566, respectively. The errors of filling factor, height and profile shape have a big influence on the average transmittance. The transmittance of the ZnSe microstructure with coned profile shows some regular distribution with the increase of structure height and the number of divided layers, and it has a great improvement as compared with the optimized columned ZnSe micro-structure.