The influence of crystallographic orientation on the nanomechanical properties of 50 nm thick (100)-oriented single-crystal silicon resonators was investigated by examining the effects of surface treatments, such as flash-heating, on the mechanical quality factors (Q-factors) and resonant frequencies. The measured Q-factors were found to vary periodically with crystallographic orientation and were shown to have higher values in the 〈110〉 direction. A 1500 nm thick (100)-oriented cantilever array was also studied for comparison, for which no obvious periodic change was observed. Since the energy dissipation in vibrating resonators cannot be explained by the support loss or thermoelastic loss, a surface-related mechanism should be considered.