Three-dimensional memory device with self-aligned drain select level isolation structures and method of making thereof

A three-dimensional memory device includes an alternating stack of insulating layers and electrically conductive layers located over a substrate. An insulating fill material layer and drain select gate electrodes are located over the alternating stack. A group of memory stack structures extends through the alternating stack, and is arranged as rows of memory stack structures. Each memory stack structure is entirely encircled laterally by a respective one of the drain select gate electrodes. The insulating fill material layer includes a drain select level isolation structure extending between neighboring rows of memory stack structures and including a pair of sidewalls containing a respective laterally alternating sequence of planar vertical sidewall portions and concave vertical sidewall portions, and a drain select level field portion adjoined to the drain select level isolation portion.