The microstructure morphologies of copper bonded wafers were examined by means of transmission electron microscopy (TEM) and atomic force microscope (AFM). Morphologies of non-distinct, zigzag and distinct interfaces in the bonded layer are observed. A strong relationship between the roughness of surfaces and the individual steps in bonding initiation was found. We propose three different mechanisms to explain the observed morphologies. In addition, the role of atomic diffusion and that of annealing effects during bonding is discussed.