A method of manufacturing a 3D semiconductor device, the method including forming a first target structure, the first target structure including at least one upper gate, at least one bottom gate, and a dielectric separation layer disposed between and separating the at least one upper gate and the at least one bottom gate; removing material in a plurality of material removal areas in the first target structure, the plurality of material removal areas including at least one material removal area that extends through the at least one upper gate to a top of the dielectric separation layer; and forming a first contact establishing a first electrical connection to the upper gate and a second contact establishing a second electrical connection to the at least one bottom gate, such that the first contact and second contact are independent of each other.