A depth-controlled process for the tip-based etching of highly ordered pyrolytic graphite has been developed. This process provides unprecedented control on the dimensional parameters of the structures. Arrays of over 100 structures have been fabricated with strict tolerances on the placement, depth, and size of each feature. Custom software provides closed-loop depth control as well as the ability to change the fabrication parameters on-demand, immediately before each feature is made. To date, protrusions, holes, trenches, and even words have been patterned on scales ranging from 1 nm2 to 1 mm2 and depths ranging from sub nm to as deep as 200 nm. A 1.5 mu-m2 array of 100 holes was fabricated. The average hole depth was 19.9 nm +/- 2.2 nm and the average width was 32.2 nm +/- 4.4 nm. Additionally, an array of 105 trenches with two different lengths was fabricated. The array was 3.2 mu-m across and 2.2 µm down. The pitch in the x direction was 350 nm and in the y direction was 155 nm. The two lengths present in the array had an average value of 136 nm for the short lines and 183 nm for the long lines with a variation of 4.4% and 2.7% respectively.