A method for fabricating a semiconductor device includes forming a through-hole penetrating through an alternating stack pattern and forming a gap-fill layer, wherein a sacrificial gap-fill layer of the gap-fill layer fills the through-hole. The method also includes forming a mask layer over the alternating stack pattern and over the gap-fill layer, wherein the mask layer includes a self-aligned opening overlapping the filled through-hole and overlapping a portion of an uppermost material layer of the alternating stack pattern adjacent to the filled through-hole. The method further includes forming a first contact hole through the alternating stack pattern by performing a single etch using both the mask layer and the portion of the uppermost material layer as etch barriers to remove, through the self-aligned opening, the sacrificial gap-fill layer filling the through-hole.