Raman spectra of large graphene bubbles showed size-dependent oscillations in spectral intensity and frequency, which originate from optical standing waves formed in the vicinity of the graphene surface. At a high laser power, local heating can lead to oscillations in the Raman frequency and also create a temperature gradient in the bubble. Based on Raman data, the temperature distribution within the graphene bubble was calculated, and it is shown that the heating effect of the laser is reduced when moving from the center of a bubble to its edge. By studying graphene bubbles, both the thermal conductivity and chemical reactivity of graphene were assessed. When exposed to hydrogen plasma, areas with bubbles are found to be more reactive than flat graphene.