A method of fabricating a semiconductor device includes providing a substrate including a first region and a second region. The method includes forming a first layer on the substrate. The first layer has a first hole on the first region and a second hole on the second region. The method includes forming a second layer in the first hole and the second hole. The method includes forming a mask pattern on the second region of the substrate. The method includes polishing the second layer to form a pattern in the first hole and an overlay key pattern in the second hole. A top surface of the overlay key pattern is further from the substrate than a top surface of the pattern in the first hole.