Creation of micro dimples on material surface is significant for their functional applications. Because of unique properties, metallic glasses are regarded as emerging structural and functional materials but they are also a kind of difficult-to-cut materials due to high hardness and easy to crystallization and oxidation. In this study, a new method was proposed to fabricate micro dimples on metallic glass surface, which consisted of two steps, nanoindentation experiments to form the pre-indent array followed by polishing. Via this two-step method, square and rectangle dimples were successfully formed which exhibited multi-scale features with one relatively large dimple with width in micron-scale and depth in nanometer-scale, together with relatively small residual indents in nanometer-scale distributed on its bottom surface. The experimental results indicated that the depth of multiscale dimples was affected by the spatial interval between two indents and the polishing time. Under the used experimental conditions, for the same polishing time, the depth of the large dimple was decreased when increasing the interval; for the same interval, with increase in the polishing time, the depth of the large dimple was also decreased. The possible formation mechanism of the large dimple was discussed, which was mainly ascribed to the enhanced material removal at the position of pre-indent array because of the concentration of polishing particles by the pre-indents.