A method has been developed to probe the localized inhomogeneities of acids in thin 193 nm polymer photoresist films using nanomolar concentrations of the pH-sensitive fluorophore Cournarin 6 (C6). C6 exhibits distinct absorption and emission wavelengths for its neutral and protonated forms, allowing the fluorescence for each species to be separated into two distinct detection channels and imaged spatially using two-color confocal microscopy. A two-dimensional thresholding technique was used to distinguish between signal and noise. The ratio (R) of the two intensity channels indicates the degree to which each C6 molecule is protonated, and distributions of these values can be used to describe the relative inhomogeneity in the polymer system for samples with a given average acid concentration. For ensemble measurements of C6 in solution, a single narrow distribution of R-values was obtained. Photoresist film samples prepared from solutions with bulk pH near the pK(a) of C6 exhibit broad bimodal distributions centered about the expected mean R-value (R = 1). We infer from this result that in these polymer films, at temperatures below the glass transition, proton exchange happens on a very slow time scale. In this case the state of the fluorophore is effectively frozen as either neutral or protonated.