A method and structure that forms a multilayer nanoparticle thin film assembly begins by functionalizing a substrate with functional molecules. Next, the invention replaces a stabilizer on a bottom surface of the first nanoparticles with the functional molecules via surface ligand exchange to make a first nanoparticle layer on the substrate. The invention then replaces the stabilizer on a top surface of the first nanoparticle layer with functional molecules via surface ligand exchange. The invention replaces the stabilizer on a bottom surface of the second nanoparticles with the functional molecules via surface ligand exchange to make a second nanoparticle layer on the first nanoparticle layer. Lastly, the invention repeats the previous steps and forms additional nanoparticle layers.