A method for marking an ophthalmic lens with a hydrophobic and/or oil-repellent low surface energy outer layer on a high surface energy substrate or coating. The method consists in: positioning a complementary patterning mask of the desired marking between the lens surface to be marked and an energizing discharge source capable of substantially eliminating the outer layer to as to expose the subjacent high energy substrate or coating. The temporary protective layer has a surface energy higher than that of the outer layer and a thickness less than about 5 nm, and preferably between 2 and 4 nm, thereby enabling the discharge to act on the outer layer through the temporary protective layer.