For microseparation devices, the quality of the microholes, e.g., smooth surfaces and edges, is of crucial importance for high-performance separating ability. Here, we used water-assisted femtosecond laser perforating technology to fabricate high-quality size-controllable (from several to tens of micrometers) micropore arrays on ultrathin aluminum foil surface, which have smooth edges without fragments and debris. The micropore arrays can effectively filtrate particles with diverse diameters. Compared to the micropores prepared in air under the same laser processing parameters, the water-assisted micropores have greatly improved the surface quality, and the particle separation ratio can be increased by ∼40 % . This method for preparing high-quality micropore arrays can also be applied to other sheet materials, such as titanium, silicon, and even plastic, and so on, which can be widely used in the fields of microfluidic devices for microseparation.