A method of manufacturing a semiconductor device includes forming a first alignment mark trench in a first material layer on a substrate. A first alignment mark via may then be formed by etching a second material layer that is underneath the first material layer, where the first alignment mark via is positioned to communicate with the first alignment mark trench. Then, a trench-via-merged-type first alignment mark may be formed by filling the first alignment mark trench and the first alignment mark via with a light reflection material layer.