Ion-flow-stimulated roughening transition is a phenomenon that may prove useful in the hierarchical structuring of nanostructures. In this work, we have investigated theoretically and experimentally the surface texturing of single-crystal and multi-crystalline silicon wafers irradiated using ion-beam flows. In contrast to previous studies, ions had relatively low energies, whereas flow densities were high enough to induce a quasi-liquid state in the upper silicon layers. The resulting surface modifications reduced the wafer light reflectance to values characteristic of black silicon, widely used in solar energetics. Features of nanostructures on different faces of silicon single crystals were studied numerically based on the mesoscopic Monte Carlo model. We established that the formation of nano-pyramids, ridges, and twisting dune-like structures is due to the stimulated roughening transition effect. The aforementioned variety of modified surface morphologies arises due to the fact that the effects of stimulated surface diffusion of atoms and re-deposition of free atoms on the wafer surface from the near-surface region are manifested to different degrees on different Si faces. It is these two factors that determine the selection of the allowable "trajectories" (evolution paths) of the thermodynamic system along which its Helmholtz free energy, F, decreases, concomitant with an increase in the surface area of the wafer and the corresponding changes in its internal energy, U (dU>0), and entropy, S (dS>0), so that dF=dU - TdS<0, where T is the absolute temperature. The basic theoretical concepts developed were confirmed in experimental studies, the results of which showed that our method could produce, abundantly, black silicon wafers in an environmentally friendly manner compared to traditional chemical etching.