We develop an innovative manufacturing process, based on radio-frequency magnetron sputtering (RFMS), to prepare neat CdSe quantum dots (QDs) on glass and silicon substrates and further chemically functionalize them. In order to validate the fabrication protocol, their optical properties are compared with those of QDs obtained from commercial solutions and deposited by wet chemistry on the substrates. Firstly, AFM measurements attest that nano-objects with a mean diameter around 13 nm are located on the substrate after RFMS treatment. Secondly, the UV-Vis absorption study of this deposited layer shows a specific optical absorption band, located at 550 nm, which is related to a discrete energy level of QDs. Thirdly, by using two-color sum-frequency generation (2C-SFG) nonlinear optical spectroscopy, we show experimentally the functionalization efficiency of the RFMS CdSe QDs layer with thiol derived molecules, which is not possible on the QDs layer prepared by wet chemistry due to the surfactant molecules from the native solution. Finally, 2C-SFG spectroscopy, performed at different visible wavelengths, highlights modifications of the vibration mode shape whatever the QDs deposition method, which is correlated to the discrete energy level of the QDs. (C) 2015 Elsevier Inc. All rights reserved.