We report a simple method for the fabrication of a poly(dimethylsiloxane) (PDMS) membrane with through-holes by blowing a residual prepolymer away from a photoresist (PR)-patterned Si wafer. The fabrication method for the perforated polymer membrane is crucial to achieve both complicated three-dimensional microfluidic devices and polymer sieve sheets. This method has several advantages over the previous methods in that we can repeatedly make the well-defined holes on the PDMS membranes even if the excess prepolymer remains on the PR mold after spincoating at a relatively low rpm. In addition, the desired pattern can be selectively perforated from the whole wafer even if the mold is fabricated by single-step lithography.