Coating nano/micro-structured elements with a single or multi-layered film can greatly enhance their functionality. The experimental enhancement, however, is significantly limited by the smoothing and distortion of the structural profile after coating. This requires a comprehensive understanding of the layer growth behavior on nanoscale non-isotropic surface with a proper model to analyze and predict the structure evolution. Here, a simplified linear growth model with single free parameter was successfully used for analysis of the smoothening of grating grooves. The model enables a quantitative description of the evolution of surface morphology from substrate to the top surface with sub-nanometer accuracy. Based on this, the smoothing behavior of single-Si layer and W/Si multilayer growth on nanoscale gratings (period ∼ 40 nm) and flat substrates were studied experimentally, for applications in X-ray optics. The smoothing effect of the W/Si multilayer coating is more pronounced than that of the single Si layer for both substrate types. The corrugated nanogratings suppressed the smoothing effect as compared to the flat isotropic surface. These works provide new guidance to predict and control the growth of layers on nanostructures.