Atomic force microscopy has been used to examine the effect of surface morphology on the formation of HxMoO3 during the reaction of MoO3 with methanol. By heating MoO3 crystals in hydrous environments, pits can be formed on the (010) surface. We have found that pit formation is activated by elastic strain from extended defects and because of this, it is possible to exercise some degree of control over the density, crystallography, and size of these features. This phenomenon was exploited to create different and well characterized morphological features on pairs of mated surfaces, cleaved from the same single crystal. The mated pairs were then reacted simultaneously in methanol-N-2 mixtures at temperatures between 300 and 330 degrees C. Surfaces with pits that expose (h0l) type facets containing undercoordinated Mo sites were observed to intercalate more H than relatively flat surfaces. This result, together with the observation that acicular HxMoO3 precipitates grow from the edges of the pits, suggests that the undercoordinated surface Mo on the (h0l) surfaces are active for the dissociative chemisorption of methanol at temperatures between 300 and 330 degrees C.