Doping of nanostructures, in particular semiconductor nanowires, during their synthesis is remarkably difficult due the strict control of process conditions required. Ion beam irradiation is a viable alternative as dopant incorporation it is not inherently limited by chemical potentials. However, in nanowires the sputter yield obtained during ion irradiation is large, because of the large surface to volume ratio. The nanowire diameter and ion energy dependency of the sputter yield can be qualitatively understood by the Sigmund model for sputtering. Monte-Carlo (MC) simulations using the binary collision approximation in the regime where the extent of the ion’s collision cascade in the target material is of similar order of magnitude as the nanowire diameter are confirmed by sputter yields of Si nanowires irradiated at 300 °C with 100 keV and 300 keV Ar, determined by high resolution SEM. The large sputter yield in nanowires causes a non-linear increase in the doping concentration with the irradiated ion fluence, because target material is removed simultaneously to the adding of dopants. Doping concentrations obtained by nano-XRF confirm the non-linear ion fluence dependency in ZnO nanowires irradiated with Mn. This dynamic situation cannot be reproduced with static MC simulations when the sputtered volume is equal to approximately 20 % of the material affected by the ion beam. During the ion irradiation of Si nanowires at room-temperature, heretofore unexpected plastic deformation of the Si is observed. The quantification of the deformation in high resolution SEM images and an irradiation experiment under inverted geometry clearly exclude that the deformation is driven by the momentum transferred by the impinging ion onto target atoms. The deformation rate is also not comparable to that observed in literature under the name “ion-hammering”, so that an alternative, surface tension driven model is suggested.