This study describes wire electrical discharge machining (WEDM) of carbon nanofibers (CNFs) in air. Since EDM is able to machine any conductive material, it can be used to machine CNFs without causing physical damage. WEDM was applied for leveling and patterning of CNF mats, which improves the performance of field emission of CNFs. For WEDM, a wire jig system as well as debris-removing system was developed. The machining characteristics such as the effect of voltage and capacitance were investigated. WEDM in air was used for the post processing of CNF mats with high efficiency and productivity. Compared to EDM using a single tool electrode, WEDM reduced machining time to 1/10th of the previously required time.