Surface modification using ion beam techniques is recognized as an important method for improving surface controlled properties of metallic, ceramic, and semiconductor materials. Determination of the microstructure and composition in regions located within a few hundred nanometers of the surface is essential to gaining an understanding of the mechanisms responsible for the improved properties. Analytical electron microscopy (AEM), high resolution microscopy, and microdiffraction are ideally suited for this purpose. These techniques are powerful tools for characterizing microstructure in terms of solute concentration profiles, second phase formation, lattice damage, crystallinity of the implanted layer and annealing behavior. Such analyses allow correlations with theoretical models, property measurements and results of complementary techniques. The proximity of the regions of interest to the surface also places stringent requirements on specimen preparation techniques. The power of AEM in examining the effects of ion implantation will be illustrated by reviewing the results of several investigations. A brief discussion of some important aspects of specimen preparation will also be included.