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To reduce the surface roughness of a substrate for mask blanks for extreme ultraviolet (EUV) lithography, the layers of a Mo-Si multilayer structure being deposited by magnetron sputtering were treated with an assisted ion beam. The effectiveness was analyzed by atomic force microscopy, x-ray reflection diffraction, EUV reflectivity measurements, and transmission electron microscopy (TEM). An interface analysis was performed using software that extracts the roughness profile of a Mo/Si interface from a TEM image. The results showed that the treatment produced a large reduction in both interface and surface roughness, resulting in a multilayer with better EUV performance than one formed without such treatment.