A study of damages caused by gallium focused ion beam (FIB) into III-V compounds is presented. Potential damages caused by local heating, ion implantation, and selective sputtering are presented. Preliminary analysis shows that local heating is negligible. Gallium implantation is shown to occur over areas tens of nanometers thick. Gallium accumulation as well as selective sputtering during III-V compounds milling is expected. Particularly, for GaAs, this effect leads to gallium segregation and formation of metallic clusters. Microdisk resonators were fabricated using FIB milling with different emission currents to analyze these effects on a device. It is shown that for higher emission current, thus higher implantation doses, the cavity quality factor rapidly decreases due to optical scattering losses induced by implanted gallium atoms.