The site-selective assembly of colloidal polymer particles onto laterally patterned silane layers was studied as a model system for the object assembly process at mesoscale dimensions. The structured silane monolayers on silicon oxide substrates were fabricated by a combination of liquid- and gas-phase deposition of different trialkoxysilanes with a photolithographic patterning technique. By using this method various types of surface functionalizations such as regions with amino functions next to areas of the bare silica surface or positively charged regions of a quaternary ammonium silane surrounded by a hydrophobic octadecylsilane film could be obtained. Furthermore, a triethoxysilane with a photoprotected amino group was synthesized, which allowed direct photopatterning after monolayer preparation, leading to free NH(2) groups at the irradiated regions. The different silane monolayer patterns were used to study the surface assembly behavior of carboxylated methacrylate particles by optical and scanning electron microscopy. In dependence of the assembly conditions (different surface functionalizations, pH, and drying conditions), a selective preference of the particles for a specific surface type versus others was found. Site-specific colloid adsorption could be observed also on the photosensitive silane layers after local deprotection with light. From the photosensitive silane and positively charged ammonium silane, molecularly mixed monolayers were prepared, which allowed particle adsorption and photoactivation within the same monolayer as shown by fluorescence labeling.