The formation mechanisms of cones and columns by pulsed-laser irradiation in reactive atmospheres were studied using scanning electron microscopy and profilometry. Deep etching takes place in SF6-and O-2- rich atmospheres and consequently, silicon-containing molecules and clusters are released. Transport of silicon from the etched/ablated regions to the tip of columns and cones and to the side of the cones is required because both structures, columns and cones, protrude above the initial surface. The laser-induced micro-structure is influenced not only by the nature but also by the partial pressure of the reactive gas in the atmosphere. Irradiation in Ar following cone formation in SF6 produced no additional growth but rather melting and resolidification. Subsequent irradiation using again a SF6 atmosphere lead to cone restructuring and growth resumption. Thus the effects of etching plus re-deposition that produce column/cone formation and growth are clearly separated from the effects of just melting. On the other hand, irradiation continued in air after first performed in SF6 resulted in: (a) an intense etching of the cones and a tendency to transform them into columns; (b) growth of new columns on top of the existing cones and (c) filamentary nano-structures coating the sides of the columns and cones.