A system that includes a self-assembly module and a bonding module. The self-assembly module has a liquid dispensing unit, with an applicator and a reservoir for a liquid, that dispenses the liquid onto a wafer, a wafer support, an environmental control unit, a die and wafer transport mechanism, and a processor. A method for performing the hybrid bonding includes providing a wafer, patterning the wafer to form a hydrophobic surface with a plurality of hydrophilic regions, disposing the wafer on the wafer support in the self-assembly module of the hybrid bonding system, dispensing the liquid simultaneously or in batches on the plurality of hydrophilic regions on the wafer, positioning dies on the plurality of hydrophilic regions on the wafer, controlling the humidity and bonding the dies to the wafer using a hybrid bonding process.