In a method of manufacturing a semiconductor device, a front end of line (FEOL) process may be performed on a semiconductor substrate to form a semiconductor structure. A back end of line (BEOL) process may be performed on the semiconductor substrate to form a wiring structure electrically connected to the semiconductor structure, thereby formed a semiconductor chip. A hole may be formed through a part of the semiconductor chip. A preliminary plug may have a dimple in the hole. The preliminary plug may be expanded into the dimple by a thermal treatment process to form a plug. Thus, the plug may not have a protrusion protruding from the upper surface of the semiconductor chip, so that the plug may be formed by the single CMP process.