A method of manufacturing a semiconductor device includes forming a plurality of conductive lines separated from one another in a first direction via a slender hole and extending in a second direction perpendicular to the first direction, forming a first insulation layer filling the slender hole between the plurality of conductive lines, forming a plurality of first isolated holes separated from one another between the plurality of conductive lines in the first direction and the second direction by patterning the first insulation layer, forming a liner layer in the first isolated holes, filling a second insulation layer having an etching selectivity with respect to the first insulation layer, in the first isolated holes on the liner layer and forming a plurality of second isolated holes between the conductive lines by removing the first insulation layer using the etching selectivity between the second insulation layer and the first insulation layer.