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Periodic surface structures at the nanometer or micrometer scale have been achieved by various methods, while atomic-scale surface structures over large areas are unavailable. Herein, we report the formation of highly coherent atomic-scale ripple patterns on bulk metallic glass (MG) surfaces by low-energy ion irradiation. The pattern arises through three consecutive stages: emergence of initial random dots, subsequent transition to ripples, and ordering of the ripple pattern through annihilation reactions of mobile defects, while the wavelength and amplitude remain invariant throughout the patterning. No pattern is generated for the crystalline counterpart at the same irradiation condition. These observations suggest a distinct ripple forming process typical of MGs associated with their enhanced surface mobility, which enables a controllable self-organization approach for large-area surface structuring with atomic-scale precision. [ABSTRACT FROM AUTHOR]