In this work, we report on utilization and optimization of the focused-ion-beam technique for the fabrication of nanostructures on Al2O3 waveguides for applications in integrated photonic devices. In particular, the investigation of the effects of parameters such as ion-beam current, dwell time, and scanning strategy is addressed. As a result of optimizing these parameters, excellent quality gratings with smooth and uniform sidewalls are reported. The effects of redeposition are minimized and good control of the nanostructuring process is reported. The effect of Ga+ ion implantation during the milling process on the optical performance of the devices is discussed.