We performed a high-energy and high-fluence ion implantation, expecting to fabricate micromachines. (100) Si was bombarded by 3.1 MeV Au2+ ion with a fluence of 1017/cm2 at 95 K. Then an embedded layer was extracted after chemical etching (30% KOH, at 333 K). The stoichiometric change was evaluated by both experiments and simulation using TRIDYN. The experiments showed, although qualitatively, that Au clustering occurred even at a temperature lower than had ever been reported. From a critical ion fluence, which is necessary to extract a material after etching, we estimate a local concentration to be 1.0–1.2 at. %, which caused a physicochemical change by Au doping. A probable model for the clustering is proposed. It is a nonthermal atomic transfer mechanism following the electronic excitation. Here the electronic stopping power just beneath the surface is 140 eV/Å, which is large enough to ionize valence electrons of Si. Also, a wide amorphized region supports an unstable electrostatic field, which should be produced by many odd-number member rings made of host(Si) atoms. Both ionization of Si and the unstable electrostatic field may most likely trigger the Au clustering.