We modified a glass cover slip with 3-aminopropyltrimethoxysilane (APTES), and then the surface-treated cover slip was used as a substrate to immobilize carboxylate-modified streptavidin-labeled latex beads. The formation and structure of patterned-beads on the glass cover slip was characterized by using atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM). As a result, the micro-patterned latex beads, where specific chemical binding occurred, showed strong optical and topographic signals whereas no signals were observed in the case of nonspecific binding. To further utilize our microscopic techniques, we studied DNA-nanoparticles complexes. The complex formation of DNA-attached silica nanoparticles was confirmed by gel electrophoresis. AFM images clearly showed the electrostatic interaction between negatively charged DNA and positively charged silica nanoparticles. These microscopic results also provided information about the lateral position of the beads relative to the laser excitation profile, the surrounding topography on a nanometer scale, and the relationship between the optical and the structural properties of the beads.