Block copolymer thin films require selective elimination of one of their constituent blocks to access their potential as lithographic nanopatterns. This paper demonstrates an on-substrate TEM-based approach for establishing the removal of poly(methyl methyacrylate) from vertically oriented lamellar polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) thin films and subsequent transfer to the underlying silicon by reactive ion etching. The ex situ microscopy technique presents an insight into the removal of PMMA, the etch end point, PS faceting, etch anisotropy, and residual PS thickness.