Silicon oxide nanodot arrays were fabricated using functionalizedblock copolymer templates and selective silylation. A polystyrene-b-poly(acrylic acid/acrylicanhydride) (PS-b-PAA/AN) thin film containing spherical nanodomains wasused as a template to build nanoscopic silica structures. A PS-b-PAA/AN thin film was prepared by acid-catalyzed thermal deprotection of polystyrene-b-poly(tert-butyl acrylate) on an SU-8 resist film containing a photoacid generator. Thisresulting film has excellent solvent and thermal resistance due to crosslinked anhydridelinkages in carboxyl-functionalized PAA/AN block domains. Silicon was introduced byspin-spraying of hexamethyldisilazane (HMDS) over the entire surface of a self-assembled PS-b-PAA/ANthin film. HMDS was selectively reacted with carboxylic acid groups in spherical domains of a PAA/ANblock. SiO2 nanodot arrays were generated by oxygen reactive ion etching.