A system for marking the different sides of a substrate so that the different sides can be identified is disclosed. A substrate holder is used for marking a substrate during the film growth process so that the different sides of the substrate can be distinguished includes a set of fingers having a groove for holding the substrate. The fingers extend over a surface of the substrate for shielding incoming material being deposited onto the surface of the substrate leaving a portion of the surface uncovered. The fingers are positioned asymmetrically. The fingers include a first finger, a second finger, and a third finger, with a distance between said first finger and said second finger is less than the distance between said first finger and said third finger and is less than the distance between said second finger and said third finger.