A method includes bonding a first wafer to a second wafer, and performing a trimming process on the first wafer. An edge portion of the first wafer is removed. After the trimming process, the first wafer has a first sidewall laterally recessed from a second sidewall of the second wafer. A protection layer is deposited and contacting a sidewall of the first wafer, which deposition process includes depositing a non-oxygen-containing material in contact with the first sidewall. The method further includes removing a horizontal portion of the protection layer that overlaps the first wafer, and forming an interconnect structure over the first wafer. The interconnect structure is electrically connected to integrated circuit devices in the first wafer.