Nano-scale pattern sapphire substrate (NPSS) used in light-emitting diodes (LEDs) was reported that could enhance their light extraction efficiency. This paper describes a novel method to fabricate sub-micrometer surface structures on sapphire substrate. This metal contact printing method can directly transferred a metal film pattern from a silicon mold to a sapphire substrate, and subsequently use the transferred metal film pattern as the etching mask for inductively coupled plasma (ICP) etching on the sapphire substrate. Because of excellent etching selectivity of the metal films, it is easy to obtain deeper etching depth on sapphire. Experimental tests have been successfully fabricated six different feature size hexagon surface structures on a 2 inch sapphire substrate and the etching depth is about 400 nm. The LED structures were grown on the patterned sapphire substrate by metal-organic chemical vapor deposition (MOCVD). The measurement forward voltages of the LEDs grown on different pattern size of the PSS were similar, and it is found that the luminous intensity was increasing with decreasing pattern size. It indicates that the pattern size of the PSS is related to the capability of light extraction, and the maximum increase intensity is 84.7% higher than conventional LEDs.