One of the challenges of surface characterization at the nano-scale is that analytical tools which are capable of topological nano-scale analysis have limited capabilities for molecular characterization. Here we present a study on molecular characterization of positive tone photo-resist films with varying exposure dose. The technique is based on secondary ion mass spectrometry, SIMS, with gold nanoparticles (e.g. Au4+400). In the methodology a sequence of individual gold nanoparticles is used to stochastically bombard the photoresist films, where each impact results in the emission of ions from a region 10-20 nm in diameter. The technique has several unique features which enable molecular characterization at the nano-scale. Firstly, the use of individual massive clusters impacts which sample nano-volumes, and from these nano-volumes multiple molecular ions can be ejected simultaneously. Secondly, the acquisition of the mass spectra from each projectile impact allows co-ejected ions to be collected in the same mass spectrum. These two features allow for tests on the nano-scale homogeneity of molecules. This is of particular interest for photoresist films, where nano-scale inhomogeneity may result in poor quality films. In this study we examined bulk photoresist films with varying dose post development, in order to probe physical aggregation and chemical transformation on the partially exposed resist pattern side wall and surface. We found that the cation and anion of the photoacid generator were not removed equally during development, and we found that the quencher is not completely removed by the developer.