Thermal spray layers are formed on rough surfaces; however, the flattening process on rough surfaces has not yet been clarified. A mathematical flattening model which takes into account the roughness of the substrate or previously coated layers is proposed in this paper. As a result of surface roughness, the flattening degree and the flattening time decrease with increasing surface roughness in this model. In addition, the characterization of surface roughness is introduced for the flattening model. Several calculated cases of the flattening model are shown.