Silicon dioxide (SiO2) nanodot arrays were fabricated by the selective adsorption of amine-terminated polydimethylsiloxane on functionalized block copolymer thin films. A polystyrene-b-poly(acrylic acid/acrylic anhydride) thin film was created by the acid-catalyzed thermal deprotection of polystyrene-b-poly(tert-butyl acrylate). The amine-terminated polydimethylsiloxane selectively adsorbed on poly(acrylic acid) (PAA)/(acrylic anhydride) (AN) spherical nanodomains using a simple dipping method. Patterned SiO2 nanodot arrays were also fabricated using polystyrene-b-poly(tert-butyl acrylate) coated on the patterned SU-8 film. The final SiO2 nanodot arrays were obtained by the calcination of an organosilicon film.