In a wafer bonding process, one or both of two wafer substrates are scored prior to bonding. By creating slots in the substrate, the wafer's characteristics during bonding are similar to that of a thinner wafer, thereby reducing potential warpage due to differences in CTE characteristics associated with each of the wafers. Preferably, the slots are created consistent with the singulation/dicing pattern, so that the slots will not be present in the singulated packages, thereby retaining the structural characteristics of the full-thickness substrates.