Here, we present a methodology for identifying and characterizing nanoscale sites in extreme ultraviolet (EUV) photoresists that deviate from the mean composition by 3σ. The methodology is based on nano-projectile secondary ion mass spectrometry (SIMS) operating in the event-by-event bombardment detection mode. Nanoscale analysis is achieved by probing the surface stochastically with a suite of individual nanoprojectile impacts in which each nano-projectile samples a volume that is 10 to 15 nm in diameter and up to 10 nm in depth. For each impact, the coemitted secondary ions are collected and mass-analyzed, allowing for the analysis of colocalized moieties. We applied this technique to study the fundamental processes occurring in partially developed positive-tone EUV resists, which simulate a critical problem in EUV resists, incomplete resist removal, and production of line edge features. Such features erode device yield and have been the focus of many previous studies. Using NP-SIMS, we examined the changing molecular composition in the partially developed resist and isolated measurements with a probability below 0.3%. Grouping measurements based on the number and type of detected molecular species allowed for the identification of rare sites on the surface that deviate from the mean composition. The mass spectrometry measurements showed that both the photoacid generator (PAG) cation and anion displayed decreased homogeneity on average with increasing exposure dose. The effect was more pronounced in the sites with probabilities below 0.3%, where the measured intensity of the PAG-related ions in these sites was more than twofold larger than the mean. Thus, we attribute these nanoscale sites to aggregations of PAG within the top 10 nm of the remaining film. These results suggest that identifying and characterizing the molecular composition of rare sites may be important in defect production and film stochastics.