Organic monolayers anchored to silicon surfaces via silicon-carbon covalent bonds were prepared by wet process and 2D-patterning of the surface was done by local oxidation with an atomic force microscope (AFM). The surfaces were anodized with a contact-mode AFM by applying a positive bias voltage to the surface with respect to the platinum-coated cantilever under ambient conditions, which resulted in nanometer-scale oxidation of the surfaces. The anodized areas were etched and terminated with hydrogen atoms by NH₄F solution, in which various molecules having C=C bonds could be immobilized. We put allylamine molecules to which organic dyes such as fluorescein and porphyrin were anchored by chemical reactions. The intensity of luminescence varied depending on dopant concentration of the substrates possibly due to energy transfer between the dyes and substrates. The method demonstrated here is one of the promising way to fabricate 3 D-assemblies of molecular scale electronic devices on silicon with a stable interface.