The self-organizing map with relational perspective mapping (SOM-RPM) is an unsupervised machine learning method that can be used to visualize and interpret high-dimensional hyperspectral data. We have previously used SOM-RPM for the analysis of time-of-flight secondary ion mass spectrometry (ToF-SIMS) hyperspectral images and three-dimensional (3D) depth profiles. This provides insightful visualization of features and trends of 3D depth profile data, using a slice-by-slice view, which can be useful for highlighting structural flaws including molecular characteristics and transport of contaminants to a buried interface and characterization of spectra. Here, we apply SOM-RPM to stitched ToF-SIMS data sets, whereby the stitched data are used to train the same model to provide a direct comparison in both 2D and 3D. We conduct an analysis of spin-coated polyaniline (PANI) films on indium tin oxide-coated glass slides that were subjected to heat treatment under atmospheric conditions to model PANI as a conformal aerospace industry coating. Replicates were shown to be precisely equivalent, both spatially and by composition, indicating a clear threshold for annealing of the film. Quantitative assessment was performed on the chemical breakdown trends accompanying annealing based on peak ratios, while spectral analysis alone shows only very subtle differences which are difficult to evaluate quantitatively. The SOM-RPM method considers data sets in their totality and highlights subtle differences between samples often simply differences in peak intensity ratios.