Methods and apparatus for forming a germanium containing film on a patterned substrate are described. The patterned substrate is a silicon, or silicon containing material, and may have a mask material formed on a surface thereof. The germanium containing material is formed selectively on exposed silicon in the recesses of the substrate, and an overburden of at least 50% is formed on the substrate. The germanium containing layer is thermally treated using pulsed laser radiation, which melts a portion of the overburden, but does not melt the germanium containing material in the recesses. The germanium containing material in the recesses is typically annealed, at least in part, by the thermal treatment. The overburden is then removed.