Nanolithography with self‐assembled block copolymers (BCPs) is an emerging competitive alternative to conventional lithography, which is currently reaching its limits with regard to resolution and economic feasibility. For high‐resolution lithography, both the abruptness of BCP internal interfaces between self‐assembled polymer nanodomains and the processing steps used to selectively remove one of the polymers are crucial. This paper presents a detailed investigation of the chemistry, the mask wall morphology, and the line edge roughness (LER) of self‐assembled nanomasks from polystyrene‐b‐polymethylmethacrylate (PS‐b‐PMMA) before and after selective removal of the PMMA nanodomains. For the latter, either wet or plasma etching are employed and their impact on both the morphology and chemistry of resulting nanomasks is analysed using analytical (scanning) transmission electron microscopy (STEM), X‐ray photoelectron spectroscopy and polarization‐modulated infrared reflection‐absorption spectroscopy. Dedicated image analysis tools are developed to determine for the first time the LER of cylindrical openings in PS masks from STEM dark‐field images at sub‐nanometer resolution. Applying these tools prior to and after PMMA removal from the BCP films, the statistics of feature sizes, LERs, and interfacial widths are determined. In addition, the impact of wet and dry etching processes on PS‐co‐PMMA random copolymer brushes required for substrate functionalization is evaluated.