The damage growth and surface modifications in Si(100), induced by 25 keV Si − 5 cluster ions, as a function of fluence, φ, has been studied using atomic force microscopy (AFM) and channeling Rutherford backscattering spectrometry (CRBS). CRBS results indicate a nonlinear growth in damage from which it has been possible to get a threshold fluence, φ0, for amorphisation as 2.5 × 10 13 ions cm −2 . For φ below φ0, a growth in damage as well as surface roughness has been observed. At a φ of 1 × 10 14 ions cm −2 , damage saturation coupled with a much reduced surface roughness has been found. In this case a power spectrum analysis of AFM data showed a significant drop, in spectral density, as compared to the same obtained for a fluence, φ < φ0. This drop, together with damage saturation, can be correlated with a transition to a stress relaxed amorphous phase. Irradiation with similar mass Cs − ions, at the same energy and fluence, has been found to result in a reduced accumulation of defects in the near surface region leading to reduced surface features.