An alternating stack of first material layers and second material layers is formed over a substrate. A hard mask layer is formed over the alternating stack. Optionally, an additional hard mask layer can be formed over the hard mask layer. A photoresist layer is applied and patterned, and cavities are formed in the hard mask layer by performing a first anisotropic etch process that transfers a pattern of the openings in the photoresist layer through the hard mask layer. Via openings are formed through an upper portion of the alternating stack by performing a second anisotropic etch process. A cladding liner can be optionally formed on sidewalls of the cavities in the hard mask layer. The via openings can be vertically extend through all layers within the alternating stack by performing a third anisotropic etch process.