A Y-shaped carbon nanotube atomic force microscope probe tip and methods comprise a shaft portion; a pair of angled arms extending from a same end of the shaft portion, wherein the shaft portion and the pair of angled arms comprise a chemically modified carbon nanotube, and wherein the chemically modified carbon nanotube is modified with any of an amine, carboxyl, fluorine, and metallic component. Preferably, each of the pair of angled arms comprises a length of at least 200 nm and a diameter between 10 and 200 nm. Moreover, the chemically modified carbon nanotube is preferably adapted to allow differentiation between substrate materials to be probed. Additionally, the chemically modified carbon nanotube is preferably adapted to allow fluorine gas to flow through the chemically modified carbon nanotube onto a substrate to be characterized. Furthermore, the chemically modified carbon nanotube is preferably adapted to chemically react with a substrate surface to be characterized.