A method for forming a pad in a wafer with a three-dimensional stacking structure is disclosed. The method includes bonding a device wafer that includes an Si substrate and a handling wafer, thinning a back side of the Si substrate, depositing an anti-reflective layer on the thinned back side of the Si substrate, depositing a back side dielectric layer on the anti-reflective layer, forming vias that pass through the anti-reflective layer and the back side dielectric layer and contact back sides of super contacts which are formed on the Si substrate, and forming a pad on the back side dielectric layer such that the pad is electrically connected to the vias.