Block copolymer lithography allows for the large-area patterning of surfaces with self-assembled nanoscale features. The created nanostructured polymer films can be applied as masks in common lithography processing steps, such as lift-off and etching for pattern replication and transfer. In this work, we discuss an approach to improve the pattern replication efficiency by modification of the polymer mask prior to lithographical use by means of an O2/Ar plasma treatment. We present a much better quality of pattern replication without loss of features, along with a precise tunability of feature sizes, that can be achieved by short mask treatment. We point out a correlation between nanopore position within the ordered arrays, expressed by its coordination number, the nanopore shape and the replication efficiency. Our experimental strategy to explain these correlations combines the indirect investigation of patterns replicated from the modified polymer masks and direct investigation of the mask top and bottom. Pattern replication is performed either in the form of gold nanodot arrays created via lift-off or nanopores transferred into a SiO2 substrate by reactive ion etching. The direct analysis of free polymer membranes released from the substrate reveals the nanopore shape at the mask top and bottom surfaces.