Atomic scale modifications and subsequent atomic resolution imaging has been achieved on the highly oriented pyrolytic graphite surface in air. Application of short pulse voltages, above a minimum threshold voltage of 3.5 V, across the tunneling gap results in the displacement of a layer or more of atoms to form a hole and create a neighboring mound or "nanodot" from the displaced atoms. We have found a correlation between the hole and "nanodot" volume at the atomic level and observe an asymmetric displacement of material in all cases of feature creation. Nanofeatures as small as four carbon atoms at beta sites have been created. Our experimental observations are consistent with the modification process depending on the gradient in the electric field induced by the rise time of the bias pulse voltage and not the pulse duration. Interesting faceting behavior has also been observed around some hole edges. Tip bias pulsing sometimes induced a tip, and not a surface modification, resulting in a change in the observed tunneling image.