The understanding of surface properties of core-shell type nanoparticles is important for exploiting the unique nanostructured catalytic properties. We report herein findings of a spectroscopic investigation of the thermal treatment of such nanoparticle assemblies. We have studied assemblies of gold nanocrystals of similar to2 nm core sizes that are capped by alkanethiolate shells and are assembled by covalent or hydrogen-bonding linkages on a substrate as a model system. The structural evolution of the nanoparticle assemblies treated at different temperatures was probed by several spectroscopic techniques, including UV-visible, Fourier transform infrared (FTIR), and X-ray photoelectron spectroscopy (XPS). The results show that the capping/linking shell molecules can be effectively removed to produce controllable surface and optical properties. The data further revealed that the thermally induced evolution of the surface plasmon resonance property of gold nanoparticles is dependent on the chemical nature of the linker molecule. The spectral evolution is discussed in terms of changes in particle size, interparticle distance, and dielectric medium properties, which has important implications for controlled preparation and thermal processing of core-shell nanostructured metal catalysts.