Structural changes of Si(100) locally milled by a 8 keV Ga+focused ion beam were investigated with SEM and TEM. A Ga+beam was focused on a thin section of a TEM specimen and at room temperature made a hole of about 10 μm. The observations were carried out at the region adjacent to the hole. The results of SEM and TEM indicated that a beam affected zone was formed surrounding the hole, where Ga was detected by EDS. TEM photographs also showed flakes of Ga-related film with an orientation relationship with the Si(100) matrix spread in this regime. Analysis of the electron diffraction pattern and the phase relationship of the Si-Ga system indicated the possibility of these flakes being the metastable Ga phase which had interplanar spacing larger than 0.3 nm.