A method of aligning carbon nanotubes (CNTs) and a method of manufacturing a field emission device (FED) using the same, wherein a mold having an intaglio pattern is prepared, an aqueous solution containing an amphiphilic organic material and the CNTs are coated on a surface of a substrate, the mold is adhered to the substrate surface to cause the aqueous solution to flow into the intaglio pattern by a capillary force, and the mold is removed from the substrate surface to vertically align the CNTs on the substrate surface.