Single crystalline Al crystals were bonded via surface activated bonding at room temperature with the crystallographic orientation of (111)parallel to(111) and [110]parallel to[110]. The interfacial microstructure was investigated by high-resolution transmission electron microscopy (TEM) to investigate the process of the interface formation of the system. The interface was found to form first between the tops of the protrusions which existed on the Al surfaces as roughness before bonding. At those formed bonded regions, no intermediate and damage layer was observed in the lattice images. It means that the fast atom beam irradiation used for surface activation of the metal surfaces does not alter the surface crystallinity as far as TEM observation allows. The bonded regions, however, exhibited a different contour from what could be conjectured without taking atomic rearrangement into consideration. This change in the geometrical configuration indicates that the protrusions had deformed during the bonding procedure. Microscopically, however, no disordering of the lattice was seen near the interface. Therefore, it is concluded that the heads of the protrusions have deformed plastically and then rearrangement of the atoms took place. Moreover, the defects found at the interface exhibit a delocalized core structure, indicating that the interface should have a relaxed structure.