This paper describes the direct write laser fabrication of a photolithography mask for prototyping of microfluidic devices in polydimethylsiloxane. An amplified femtosecond pulse laser is used to selectively remove the aluminium metal layer from the poly(methyl methacrylate) photomask substrate. The use of a femtosecond pulse laser to selectively etch a metal layer has several advantages over other conventional methods for binary photomask fabrication, namely rapid prototyping of microfluidic devices using soft lightography. Control of the energy density and defocus position of the focusing objective lens results in the etching of features with widths ranging from 2 µm to 35 µm when using an objective lens with a numerical aperture of 0.25.