A method for patterning an epitaxial substrate includes: (a) forming an etch mask layer over an epitaxial substrate, and patterning the etch mask layer using a patterned cover mask layer to form the etch mask layer into a plurality of spaced apart mask patterns; and (b) etching the epitaxial substrate that is exposed from the mask patterns, and removing the mask patterns such that the epitaxial substrate is formed with a plurality of spaced apart substrate patterns.