Single wavelength ellipsometry and atomic force microscopy (AFM) have been applied in a well-calibrated beam-etching experiment to characterize the dynamics of surface roughening induced by chemical etching of a similar to12 nm amorphous silicon (a-Si) top layer and the underlying crystalline silicon,(c-Si) bulk. In both the initial and final phase of etching, where either only a-Si or only c-Si is exposed to the XeF2 flux, we observe a similar evolution of the surface roughness as a function of the XeF2 dose proportional to D(XeF2)(beta) with beta approximate to 0.2. In the transition region from the pure amorphous to the pure crystalline silicon layer, we observe a strong anomalous increase of the surface roughness proportional to D(XeF2)(beta) with beta approximate to 1.5. Not only the growth rate of the roughness increases sharply in this phase, also the surface morphology temporarily changes to a structure that suggests a cusplike shape. Both features suggest that the remaining a-Si patches on the surface act effectively as a capping layer which causes the growth of deep trenches in the c-Si. The ellipsometry data on the roughness are corroborated by the AFM results, by equating the thickness of the rough layer to 6 sigma, with sigma the root-mean-square variation of the AFM's distribution function of height differences. In the AFM data, the anomalous behavior is reflected in a too small value of sigma which again suggests narrow and deep surface features that cannot be tracked by the AFM tip. The final phase morphology is characterized by an effective increase in surface area by a factor of two, as derived from a simple bilayer model of the reaction layer, using the experimental etch rate as input. We obtain a local reaction layer thickness of 1.5 monolayer consistent with the 1.7 ML value of Lo et al. [Lo et al., Phys. Rev. B 47, 648 (1993)] that is also independent of surface roughness. (C) 2005 American Vacuum Society.