This paper reports a new type of soft PDMS/metal-film photo-mask which can be applied in contact photolithography with a resolution at sub-micrometer scale and a patterning area over a 4 wafer. This new type of photo-mask is made from a soft PDMS mold which contains a patterned metal film on the concave surface of its microstructures. The metal film can selectively block incident UV light, while the convex PDMS microstructures can guide the incident UV light to expose a PR layer. Due to its soft and compliant property, this new soft photo-mask can from intimate contact with a substrate and carry out UV exposure to form PR microstructures. It is particularly useful in patterning slightly curved substrates such as sapphire wafers, and therefore has a great potential on manufacturing patterned sapphire substrates (PSSs) in light-emitting diodes (LEDs). In this wok, both 2 and 4 PSSs with sub-micrometer feature sizes are successfully achieved. This new type of soft photo-mask and its contact photolithography can be easily implemented at a low cost for large-area, non-flat, and sub-micrometer scaled patterning, and therefore has a great potential in many applications in the future.