A silicon-containing nucleation layer can be employed to provide a self-aligned template for selective deposition of tungsten within backside recesses during formation of a three-dimensional memory device. The silicon-containing nucleation layer may remain as a silicon layer, converted into a tungsten silicide layer, or replaced with a tungsten nucleation layer. Tungsten deposition can proceed only on the surface of the silicon-containing nucleation layer or a layer derived therefrom in a subsequent tungsten deposition process.