Si nanopillars of less than 50 nm diameter have been irradiated in a helium ion microscope with a focused Ne$^+$ beam. The morphological changes due to ion beam irradiation at room temperature and elevated temperatures have been studied with the transmission electron microscope. We found that the shape changes of the nanopillars depend on irradiation-induced amorphization and thermally driven dynamic annealing. While at room temperature, the nanopillars evolve to a conical shape due to ion-induced plastic deformation and viscous flow of amorphized Si, simultaneous dynamic annealing during the irradiation at elevated temperatures prevents amorphization which is necessary for the viscous flow. Above the critical temperature of ion-induced amorphization, a steady decrease of the diameter was observed as a result of the dominating forward sputtering process through the nanopillar sidewalls. Under these conditions the nanopillars can be thinned down to a diameter of 10 nm in a well-controlled manner. A deeper understanding of the pillar thinning process has been achieved by a comparison of experimental results with 3D computer simulations based on the binary collision approximation.
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