In this study, we propose a fabrication method of three-dimensional complex shape polydimethylsiloxane microstencils. Three-dimensional complex shape polydimethylsiloxane (PDMS) microstencils were fabricated by an air-knife system and PDMS casting form preparing master mold by photolithography, diffuser lithography and polyurethane acrylate (PUA) replication. PDMS microstencils shape was a production of the hemispherical and quadrangular pyramid. When the prepolymer of PDMS was spin-coated onto the three-dimensional complex shape master mold, a thin layer of prepolymer remained on top of the master"s structure and consequently prevented formation of perforated patterns. This residual layer was easily removed by the air-knife. The air-knife system was controlled by the flow rate of N2 gas and conveying speed of the master mold. Results revealed the fabricated three-dimensional complex shape PDMS microstencils, could be useful for application of three-dimensional cell culture device.