The invention provides improved techniques for bonding devices using copper-to-copper or other types of bonds. A substrate is cleaned to remove surface oxides and contaminants and then rinsed. The rinsed substrate is provided to coating unit where a protective coating is applied to the substrate. The protective coating may be applied by immersing the substrate in a bath or via chemical vapor deposition. In an aspect, the protective coating may be copper selective so that the protective coating is only applied to copper features of the substrate. The protective coating minimizes formation of oxides and other bond weakening forces that may form during bonding processes, such as bonding a copper wire to a copper bond pad of the substrate. In an aspect, an annealing process is used to cure the protective coating and remove small imperfections and other abnormalities in the protective coating prior to the bonding process.