The effects of tip‐sample bias pulses while within tunneling distances have been investigated for graphite surfaces in contact with dry fluids, fluids containing water, and liquid water. In dry ambients, no surface modifications were observed at pulse voltages in excess of ±10 V. In fluids containing water, bias pulses exceeding a threshold voltage produced pits in the graphite surface, but the threshold voltage exhibited daily fluctuations of as much as 5 V. At the threshold for surface modification, a typical pit was found to have a diameter of approximately 30 A˚ and was 3 A˚ in depth. The diameter and depth of the pits increased with pulse amplitude above the observed threshold. In pure water, a reproducible bias pulse threshold of 4.0±0.2 V was observed, and such pulses yielded dome‐like features on the surface. The domed features were found to have a diameter of ∼7 A˚ and were ∼1.5 A˚ high. Bias pulses greater than 4.0 V were found to produce pits of approximately the same diameter as those produced in humid gases. Although little is known at present about the chemical structure of the domed features, their conversion into pits with subsequent bias pulses of only 0.2 V suggests that they are structural intermediates in the pit formation process. This hypothesis implies that the domed features may be vulnerable to chemical attack; consequently, the domes may present a viable route to the localized, designed, chemical functionalization of a graphite surface.