Using a micro-Contact Printing (μ-CP) technique, substrates are prepared with patterns of hydrophilic, hydroxyl-terminated SAMs and hydrophobic methyl-terminated SAMs. Beginning with a homogeneous solution of silica, surfactant, ethanol, water, and functional silane, preferential ethanol evaporation during dip-coating, causes water enrichment and selective de-wetting of the hydrophobic SAMs. Correspondingly, film deposition occurs exclusively on the patterned hydrophilic SAMs. In addition, by co-condensation of tetrafunctional silanes (Si(OR)4) with tri-functional organosilanes ((RO)3Si(CH2)3NH2), we have selectively derived the silica framework with functional amine NH2 groups. A pH sensitive, micro-fluidic system was formed by further conjugation reactions with pH sensitive dye molecules.