Embodiments of the present disclosure include self-alignment of two or more layers and methods of forming the same. An embodiment is a method for forming a semiconductor device including forming at least two gates over a substrate, forming at least two alignment structures over the at least two gates, forming spacers on the at least two alignment structures, and forming a first opening between a pair of the at least two alignment structures, the first opening extending a first distance from a top surface of the substrate. The method further includes filling the first opening with a first conductive material, forming a second opening between the spacers of at least one of the at least two alignment structures, the second opening extending a second distance from the top surface of the substrate, and filling the second opening with a second conductive material.