Provided herein may be a semiconductor device and a method of manufacturing the same. The method may include forming a second preliminary stack on a first preliminary stack; forming a first hard mask layer on the second preliminary stack; etching the first hard mask layer and forming holes through which the second preliminary stack is exposed; forming a second hard mask layer on the first hard mask layer to fill the holes; forming a linear trench by etching the second hard mask layer; forming a waved select line separation mask pattern by etching the exposed first hard mask layer; forming a select line separation trench by etching the exposed second preliminary stack using the select line separation mask pattern as an etching mask; and forming a select line separation layer by filling the select line separation trench with a non-conductor.