A method of manufacturing a semiconductor device includes providing a wafer having a first surface, wherein the wafer includes a gate electrode having a top surface, and the top surface of the gate electrode is substantially level with the first surface; and forming an alignment structure on the top surface of the gate electrode. The method further includes forming a dielectric surrounding the alignment structure on the first surface, removing the alignment structure to expose at least a portion of the top surface of the gate electrode, and forming a gate conductor over and in contact with the gate electrode.