Abstract: Hybrid bonded die stacks, related apparatuses, systems, and methods of fabrication are disclosed. One or both of an integrated circuit (IC) die hybrid bonding region and a base substrate hybrid bonding region are surrounded by a protective layer and hydrophobic structures on the protective layer. The protective layer is formed prior to pre-bond processing to protect the hybrid bonding region during plasma activation, clean test, high temperature processing, or the like. Immediately prior to bonding, the hydrophobic structures are selectively applied to the protective layer. The hybrid bonding regions are brought together with a liquid droplet therebetween, and capillary forces cause the IC die to self-align. A hybrid bond is formed by evaporating the droplet and a subsequent anneal. The hydrophobic structures contain the liquid droplet for alignment during bonding.