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Ballistic electron emission microscopy (BEEM) and deep level transient spectroscopy (DLTS) have been used to study the effects of substrate damage introduced by an ion-milling process in PtSi/n-Si Schottky contacts. Argon ions with well-defined energies of 300, 500, 700, 1000, 1500 eV were used to sputter n-type Si substrates in an ion beam sputtering system before metal deposition and silicide formation. Histograms of the PtSi/n-Si Schottky barrier height (SBH) measured by BEEM show that the mean SBH decreases with increasing ion energy, which can be explained as a result of donor-like defects that are introduced by the ion milling treatment. From DLTS measurements, we found direct evidence for the presence of such defects.