We discuss the assembly, structure, and stability of multilayer molecular films formed from multiple mercaptoalkanoic acid monolayers ligated via carboxyl and thiol interactions with divalent copper ions. Using dual-polarization interferometry to study the assembly of multilayer films in real time, we observe a clear linear relationship between the number of layers within a film and the overall average film thickness. Unexpectedly, however, we find a restructuring of the lower monolayer upon association of the Cu2+ ions to form the Cu carboxylate surface. In particular, the thickness of the lower monolayer was found to decrease significantly, accompanied by an increase in the film density. The conformation of the monolayer subsequently recovered to that observed originally following the reduction of the Cu ion to Cu+ upon chemisorption of the adlayer. Comparable restructuring was also observed in molecular dynamics simulations of a bilayer film assembled on a gold surface. Our combined experimental and theoretical study suggests that the observed restructuring is a result of charge charge interactions between adjacent Cu ions that exist in the +2 oxidation state in the copper carboxylate surface and in the +1 oxidation state following chemisorption of the adlayer.