Microfluidic lab-on-a-chip devices are usually fabricated using replica molding, with poly(dimethylsiloxane) (PDMS) casting on a mold. Most common techniques used to fabricate microfluidic molds, such as photolithography and soft lithography, require costly facilities such as a cleanroom, and complicated steps, especially for the fabrication of three-dimensional (3D) features. For example, an often-desired 3D microchannel feature consists of intersecting channels with depth variations. This type of 3D flow focusing geometry has applications in flow cytometry and droplet generation. Various manufacturing techniques have recently been developed for the rapid fabrication of such 3D microfluidic features. In this paper, we describe a new method of mold fabrication that utilizes water jet cutting technology to fabricate free-standing structures on mild steel sheets to make a mold for PDMS casting. As a proof-of-concept, we use this fabrication technique to make a PDMS chip that has a 3D flow focusing junction, an inlet for the sample fluid, two inlets for the sheath fluid, and an outlet. The flow focusing junction is patterned into the PDMS slab with an abrupt, nearly stepwise change to the depth of the microchannel junction. We use confocal microscopy to visualize the 3D flow focusing of a sample flow using this geometry, and we also use the same geometry to generate water-in-oil droplets. This alternative approach to create microfluidic molds is versatile and may find utility in reducing the cost and complexity involved in fabricating 3D features in microfluidic devices.