We characterize the subsurface thermal degradation of an inert analogue of energetic molecular crystals (Eu:Y(acac)3(DPEPO)) using a wavefront-shaping assisted bidirectional focusing microscope. This microscope provides the capability to focus inside of a heterogeneous material and measure both Raman and fluorescence spectra during thermal degradation. From these measurements we find that embedding the molecular crystal in the polymer results in improved thermal stability as the polymer acts to constrict the effects of melting, which is the primary mechanism for spectroscopic changes for this material in the temperature range explored. Additionally, we identify a significant challenge in the microscope with regards to signal arising from out of focus guidestar particles and scattering particles. To address this issue we propose the use of spatial filtering of the output signal to remove unwanted signal while keeping the in-focus signal.