Geometrical features of an alignment mark for focused ion beam (FIB) implantation in GaAs with precise alignment were studied. To optimize the etched shape on a GaAs wafer, intensity profiles of secondary electrons emitted by scanning the FIB across the mark were calculated from Monte Carlo simulation of implanted ion trajectories. The contrast and sharpness of the intensity profiles at the mark relate to the inclination angle of its sidewall and the etched depth. It was confirmed that the calculated results agreed with the experimental ones. For irradiation of 160‐keV‐Si FIB on the alignment mark with an 85° inclination angle, its etched depth of 2  μm gives the maximum contrast and sharpness. Under this condition, Si was implanted in the designated region with an alignment accuracy of 0.1 μm.