The mechanical strength properties of carbon fibers are generally thought to be correlated with the presence of underlying atomic-level defects. These defects serve to break the underlying translational symmetry of the graphitic or graphene subunits of the fiber construction, resulting in the emergence of new Raman-active spectral features. However, historical attempts to classify the precise origin of defect contributions to the Raman spectra have been challenging because of indistinct and overlapping features in the carbon fiber Raman spectra. Further, while substantial research exists on high-temperature exposure in inert atmospheres for carbon fiber composites, comparatively less addresses microscale behaviors and Raman spectral alterations to monofilament carbon fibers exposed to high-temperature atmospheric environments. Here, we report Raman spectral responses of nine commercially available high-performance, polyacrylonitrile-based carbon fibers exposed to various atmospheric heat treatments. We introduce a model-independent characterization method, the integrated absolute difference, to quantify the spectral responses to heat treatment of different fiber modulus classes. We combine this new method with a newly reported strategy to standardize spectral fitting for carbon fibers. With this approach, we show that atomic-scale defects in the underlying fiber microstructure manifest in measurably distinct manners and have distinct responses to thermal perturbation. These combined approaches may lay the foundation for disentangling contributions from specific defects in the Raman spectra of carbon fibers.