A three-dimensional memory device includes an alternating stack of insulating layers and electrically conductive layers located over a substrate, drain-select-level gate electrodes located over the alternating stack, memory openings extending through the alternating stack and a respective one of the drain-select-level gate electrodes, and memory opening fill structures located in the memory openings. The memory opening fill structures can have a stepped profile to provide a smaller lateral dimension at the level of the drain-select-level gate electrodes than within the alternating stack. Each of the drain-select-level gate electrodes includes a planar portion having two sets of vertical sidewall segments, and a set of cylindrical portions vertically protruding upward from the planar portion and laterally surrounding a respective one of the memory opening fill structures. The memory opening fill structures can be formed on-pitch as a two-dimensional array.