The newly developed method of silicon surface structuring by local desorption of passivating hydrogen with a 30 keV Si+ focused ion beam has been investigated with respect to the damage induced by the irradiation. The substrate damage was analyzed by atomic force microscopy and thermal wave analysis. The measurements show that damage can be minimized if the substrate is heated to 200 degrees C during irradiation and dwell times below 20 mu s are used for the exposure, even at a dose of 2x10(15) cm(-2), which exceeds the minimum dose required to define a feature by a factor of 10. The irradiated surfaces remain flat after KOH etching, the surface roughness being smaller than 0.3 nm for all samples.