Diffraction gratings are key elements of chirped pulse amplification laser systems. In these applications, the gratings should have high diffraction efficiency, high laser induced damage threshold (LIDT), and large spectral bandwidth. Gratings consist of grooves etched into a substrate and coated with first a highly-reflecting metallic layer and then a multilayer dielectric thin-film stack may meet these requirements. However, in reality after each layer is deposited, the new top surface of the grating deviates from the previous one, and at the end the final top surface of the grating may be significantly different from the initial substrate surface in both groove shape and groove depth. The deformation of layer interface profiles reduces the diffraction efficiency and affects the LIDT of gratings. In this work, the deformation process for a particular thin-film deposition method was studied by means of scanning electron microscopy. On the basis of the experimental data, a profile evolution model was proposed. Diffraction efficiency and bandwidth performance of metal/multilayer-dielectric coated gratings were numerically optimized for various initial substrate grating profiles by changing the dielectric layer thicknesses.