Atomic force microscopy topography and power spectral density analysis of the recorded images were used to obtain a thorough characterization of the morphological modifications determined by laser processing of Si(1-x)Ge-x/Si (100) structures grown by ultrahigh vacuum chemical vapor deposition (CVD). Two irradiation modalities were considered. In the first case, several samples differing in alloy film thickness and morphology were irradiated by KrF laser pulses at 248 nm after the CVD growth. Alternatively, the laser pulses were used to assist the CVD growth itself. In both cases laser irradiation determined primarily a severe smoothing of the surface roughness. However for the post-growth irradiation the achieved flatness was strictly dependent on the initial surface features (i.e., roughness and grain dimensions). The comparison between the results obtained in the two irradiation modalities demonstrated that, as far as surface flatness is concerned, laser-assisted deposition results a superior technique, since it allows the achievements of structureless surfaces, with roughness as low as 0.3 nm.