We monitor the structural evolution of a poly(tert-butyl methacrylate)-poly(methyl methacrylate) (PtBMA-PMMA) diblock copolymer thin film undergoing conversion via reactive annealing to yield poly(methacrylic acid)-poly(methyl methacrylate) (PMAA-PMMA). Using grazing-incidence small-angle X-ray scattering (GISAXS) and atomic force microscopy (AFM), we confirm the generation of well-ordered cylindrical micro domains in the PtBMA-PMMA precursor film after solvent annealing. After initiating thermal deprotection, the high degree of ordering can be maintained up to 25% conversion of the diblock into PMAA-PMMA. Beyond this point, a significant decrease in the overall film thickness associated with the conversion process cannot accommodate the hexagonal lattice adopted by the cylindrical microdomains. At the same time, rearrangement of PMMA cores in a PtBMA matrix that is becoming progressively glassier presents further difficulties in maintaining a reasonable structure. The fully converted PMAA-PMMA film contains a system of cylindrical microdomains that lack good ordering.