An ion microprobe system with high precision for target alignment has been realized by combining a compact scanning electron microscope (SEM) column with a target chamber. The target alignment is done first by imaging sample features with a scanning electron microscope (SEM) and then fine alignment of the sample position With respect to the incident ion beam is accomplished by comparing the secondary electron images of a Si test sample produced by the SEM beam and the ion microbeam. A Si test sample, with a specially designed relief pattern, has been used for both measuring the beam size and for determining the exact incident site of the ion beam on the target. Precision of aiming at present is about 5 mum which is limited mainly by the mechanical precision of the SEM sample holder. A beam spot size of 1.9 x 1.7 mum (FWHM) for 3 MeV He+ beam has been achieved. Use of a high precision sample manipulator affords the prospect of an ion alignment precision of about 2 mum.