Abstract We proposed an up–down working mode of electrochemical wet stamping technique (EC-WETS) for three dimensional (3D) micromachining on aluminum (Al) surface. 3D microstructures on a Si mold were transferred on to an agarose hydrogel containing 15% NaNO3, 2% MgF2, 1% NaOH and 5% glycerin, which acted as the quasi-solid electrolyte for the electrochemical micromachining. The transferred 3D microstructures on agarose hydrogel were then duplicated onto Al surface through anodic dissolution. The micromachining quality was improved by pulse-potential method dramatically with a machining tolerance lower than 200nm and an average removal rate of 210nmmin−1 in the Z direction. This method was proved to be a highly efficient, low cost and green method for 3D micromachining on active metal surface, which would be valuable for the manufacture of microelectromechanical system (MEMS).