This paper contains results of the comprehensive studies of the effect of the isotropic etching mode on roughening of the nanocomposite materials and on smoothing of the roughed nanostructure made of homogeneous materials. Three-dimensional simulation results obtained illustrate the influence of the isotropic etch process on dynamics of the roughening and smoothing of the surfaces, indicating the opposite effects of the same etch process on the surfaces made of different materials. It was shown that root mean square roughness obeys simple scaling laws during both roughening and smoothing processes. The exponential time dependences of the rms roughness have been determined.