This paper describes the use of surface chemical modification to enhance the difference of the surface charge on a patterned polyelectrolyte multilayer, which can be used for selectively adsorbing functional materials. We fabricated a patterned multilayer by combining the layer-by-layer self-assembly technique and photolithography and taking advantage of the different solubility of polyelectrolyte multilayers of diazo resins (DAR)/poly(acrylic acid) before and after UV irradiation. This patterned surface can be used as a matrix for selective adsorption of small molecular dyes, such as Methylene Blue. However the difference in surface charge on the patterned surface was not enough when we used it to selectively adsorb polystyrene (PS) nanoparticles using electrostatic force as the driving force. Therefore, we modified the patterned surface by interfacial chemistry. After modification, the patterned polyelectrolyte multilayer can be used as a good matrix for selective adsorption of PS nanoparticles with both positive and negative charges.