Surface textures, especially micro-dimple arrays, can significantly improve the friction performance of engineering parts. Through-mask electrochemical micromachining is an effective method for generating micro-dimple arrays. In this article, a new method is introduced to fabricate a large-area polydimethylsiloxane mask containing micro through-holes. Using this technique, a stainless steel mould with micro-pillar arrays is generated by wire electrical discharge machining. A combination of pressure and weight of electrolyte is then proposed to keep the polydimethylsiloxane mask closely attached to the workpiece, which helps to achieve high machining accuracy. The effects of applied voltage, effective machining time and pulse duty cycle on the micro-dimples are investigated. The profiles of the micro-dimples are not sensitive to applied voltage, but pulse duty cycle is a significant factor influencing the depth of the micro-dimples. Micro-dimples of width 95 µm, depth 19 µm and a machining area of diameter 40 mm are successfully generated using a polydimethylsiloxane mask, and the standard deviations of the micro-dimple width and depth are only 0.84 and 0.23 µm, respectively. The present experiments verify that it is feasible to obtain large-area micro-dimple arrays with high machining accuracy using this technique.