The block copolymer self-assembly approach has received great attention in recent years as a possible way to overcome the limits of conventional lithography and to fabricate sub-22 nm structures. At this level, precise nanometric control is crucial for technological applications and the search for a flexible and reproducible protocol is a great challenge. The polystyrene-b-poly(methylmethacrylate) (PS-b-PMMA) system, with a styrene fraction of 0.71, spontaneously separates into a periodic array of hexagonally packed PMMA cylinders embedded in a matrix of PS and, under suitable processing conditions, this is perpendicularly oriented with respect to the underlying substrate. The selective removal of the PMMA allows us to obtain a nanoporous PS matrix with well-defined pore dimensions. Perpendicular orientation of the PMMA cylinders requires surface neutralization by means of a suitable PS-r-PMMA random copolymer. The choice of the random copolymer is not trivial, because different PS-r-PMMA copolymers strongly affect the characteristics of the PS-b-PMMA film deposited on it. In this paper the effects of the selected PS-r-PMMA on the arrangement as well as on the peculiar dimensions (pore diameter, pore to pore distance) of the final nanoporous PS thin film are studied. Reliable protocols for the fabrication of a disposable polymeric mask are proposed in view of its application in advanced lithographic processes.