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Self-assembled monolayer (SAM) of alkane-thiol is applied on Cu damascene structures with the aim to protect the surface against contamination and oxidation prior to bonding. Three-dimensional interconnects are realized with bumpless Cu-to-Cu thermocompression bonding by wafer-on-wafer stacking. Based on cross-bar Kelvin structure measurements, up to a 17.3% reduction in the contact resistance of Cu-Cu bonds is measured with the application of SAM when the time lapse between recess and bonding is 3 h. Daisy chain with 15-μm pitch of Cu-Cu contacts is achieved with 100% bonding yield at 350°C. Ohmic contact and continuity are achieved for a maximum of 10 000 bonding contacts. The contacts are robust, and continuity of the daisy chain is preserved even after 1000 cycles of thermal stressing (-40°C to 125°C). This provides a feasible platform of high integrated circuit (IC)-to-IC connection density ( ~ 4.4 ×105 cm-2) suitable for future wafer level 3-D integration of ICs to augment Moore's law.