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This report focuses on the self organized nanostructure formation on Si (0 0 1) by erosion with low energy Kr + ions with simultaneous incorporation of metallic atoms, in particular Fe. The incorporation of Fe is thought to play an important role in the formation of some features. In the experimental set-up used here the Fe atoms come from the sputtering of a cylindrical stainless steel target situated between the source and the sample holder. It is demonstrated how the Fe flux can be regulated by operational parameters of the ion source. It is shown that two different ripple modes, one perpendicular to the ion beam projection on the surface and the other parallel, were formed at near normal incidence ( α = 20°) with ion energy between 300 eV and 2000 eV and a fluence of 6.7 × 10 18 cm −2 . The perpendicular mode ripples dominated the topography when E ion = 2000 eV, while the parallel mode ripples were the main features observed when E ion = 300 eV. The correlation of Fe concentration with ion sources parameters and resulting topography is analyzed. It is demonstrated that a certain Fe concentration is necessary for the formation of ripples that are oriented perpendicular to the ion beam and that the Fe concentration alone does not determine the evolving topography.