The demand for 3D wafer level integration has been increasing significantly. Although many technical challenges of wafer stacking are still remaining, wafer stacking is a key technology for 3D integration due to a high volume manufacturing, smaller package size, low cost, and no need for known good die. Among several new process techniques Cu-to-Cu wafer bonding is the key process to be optimized for the high density and high performance IC manufacturing. In this study two main challenges for Cu-to-Cu wafer bonding were evaluated: misalignment and bond quality of bonded wafers. It is demonstrated that the misalignment in a bonded wafer was mainly due to a physical movement of spacer removal step and the bond quality was significantly dependent on Cu bump dishing and oxide erosion by Cu CMP.