Balancing the interfacial interactions of a block copolymer (BCP) with a substrate as well as the free surface could induce the perpendicular orientation of microdomains, allowing the BCP films to serve as templates for nanofabrication. However, it has been observed that such perpendicular orientation of BCP microdomains is quite sensitive to the film thickness. We investigated the effect of film thickness on the orientation of microdomains in lamellae-forming P(S-b-MMA) thin films placed on thermally cured organosilicate (OS) substrates. For the film thickness of P(S-b-MMA) ranging from 1.25 L-0 up to 2.5 L-0, we varied the surface energy of the OS substrate around the value close to the energetically neutral condition by controlling the substrate cure temperature. We demonstrate the origin of the observed thickness effect by taking into account the increase in surface area at the free surface when the P(S-b-MMA) films make holes or islands depending on the incommensurate conditions of the BCP film. This simple but quantitative analysis allows us to define more accurate neutral windows for P(S-b-MMA) thin films in terms of both substrate surface energy and BCP film thickness.