An alternating stack of insulating layers and sacrificial material layers is formed over a substrate. Memory stack structures and a backside trench are formed through the alternating stack. Backside recesses are formed by removing the sacrificial material layers through the backside trench selective to the insulating layers. A cobalt portion is formed in each backside recess. A cobalt-semiconductor alloy portion can be formed on each cobalt portion by depositing a semiconductor material layer on the cobalt portions and reacting the semiconductor material with surface regions of the cobalt portions. A residual portion of the cobalt-semiconductor alloy formed above the alternating stack can be removed by an anisotropic etch or by a planarization process. A combination of a cobalt portion and a cobalt-semiconductor alloy portion within each backside recess can be employed as a word line of a three-dimensional memory device.