Ultraviolet irradiation (UVI) of varied duration caused cross-linking and neutralization of polystyrene (PS) homopolymers of molar mass (Mn) from 6 to 290 kg mol-1 on a silicon-oxide surface. An optimal neutral skin layer on the surface of the PS was obtained via brief UVI in air (UVIA), by which the PS had no preferential interaction with either block in the copolymer. UVI in an inert environment (gaseous dinitrogen) (UVIN) stabilized the PS layers via cross-linking and enabled the PS networks to have an effective adhesive contact with the underlying substrate. Thorough examination of domain orientations and spatial orders of a series of block copolymer, polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA), thin films deposited on these UVI-treated PS support layers yielded clear evidence that a dense layer of neutralized PS chains was required for the perpendicular orientation of PS-b-PMMA nanodomains. In particular, in addition to neutralization, two factors-the densities of physical entanglements and of chemical crosslinks-both in UVI-treated PS should be considered for the perpendicular orientation of nanolamellae and nanocylinders in symmetric and asymmetric PS-b-PMMA thin films. The density of physical entanglement in PS depends intrinsically on Mn of the PS, whereas the density of chemical cross-links was controlled with a varied duration of UVIN. Sufficiently large densities of physical entanglements and chemical cross-links can prevent PS-b-PMMA chains from penetrating through the neutral skin layer. The total density of physical entanglements and chemical cross-links required for the perpendicular orientation is correlated with the dimensions of the PS-b-PMMA chains.