Hexagonal boron nitride (hBN) plays a central role in nanoelectronics and nanophotonics. Moreover, hBN hosts room-temperature quantum emitters and optically addressable spins, making the material promising for quantum sensing and photonics. Despite significant investigation of the optical and structural properties of hBN, the role of contamination at surfaces and interfaces remains unexplored. We prepare hBN samples that are compatible with confocal photoluminescence (PL) microscopy, transmission electron microscopy (TEM), and atomic-force microscopy (AFM), and we use those techniques to quantitatively investigate correlations between fluorescent emission, flake morphology, and surface residue. We find that the microscopy techniques themselves induce changes in hBN's optical activity and residue morphology: PL measurements induce photobleaching, whereas TEM measurements alter surface residue and emission characteristics. We also study the effects of common treatments─annealing and oxygen plasma cleaning─on the structure and optical activity of hBN. The methods can be broadly applied to study two-dimensional materials, and the results illustrate the importance of correlative studies to elucidate factors that influence hBN's structural and optical properties.