Flash lamp annealing in the millisecond regime of heteroepitaxial silicon carbide on silicon structures involves melting the Si below the SiC layer, but the deep facetted nature of the solid-liquid interface leads to unacceptable surface roughness. This paper describes a method of controlling melting by implanting a high dose of carbon or germanium at a controlled depth below the Si/SiC interface, which significantly alters the melting characteristics of the silicon. Results confirm the effectiveness of these approaches for increasing surface uniformity, making liquid phase processing compatible with standard device fabrication techniques. A thermal model has also been developed to describe this process and results indicate that the theoretical work is consistent with the experimental evidence. The model is a valuable tool for predicting onset of melting, maximum temperatures and process windows for liquid phase epitaxy.