A three-dimensional memory device includes alternating stacks of insulating layers and electrically conductive layers that laterally extending along a first horizontal direction, and laterally spaced apart along a second horizontal direction by lateral isolation trenches, memory stack structures vertically extending through a respective one of the alternating stacks; and isolation trench fill structures located in the lateral isolation trenches. At least one of the isolation trench fill structures includes a first lengthwise sidewall and a second lengthwise sidewall. The first lengthwise sidewall has a first periodic lateral undulation with a uniform pitch along the first horizontal direction. The second lengthwise sidewall has a second periodic lateral undulation with the uniform pitch along the first horizontal direction.