An etching method in a semiconductor device includes forming a nitride-based first hard mask layer over a target etch layer, forming a carbon-based second hard mask pattern over the first hard mask layer, etching the first hard mask layer using the second hard mask pattern as an etch barrier to form a first hard mask pattern, cleaning a resultant structure including the first hard mask pattern, and etching the target etch layer using the second hard mask pattern as an etch barrier.