A method of treating a semiconductor substrate has forming convex patterns over the semiconductor substrate by dry etching, cleaning and modifying a surface of the convex patterns by using chemical, forming a hydrophobic functional surface on the modified surface of the convex patterns, after forming the hydrophobic functional surface, rinsing the semiconductor substrate by using water, drying the semiconductor substrate, and removing the hydrophobic functional group from the hydrophobic functional surface of the convex patterns.