Electron cyclotron resonance (ECR) argon plasma has been used to etch the native oxide on Si and thermal SiO2. The Schottky barrier height modification on both n- and p-Si has been studied as a function of substrate bias and etch time. Deep Level Transient Spectroscopy (DLTS) measurements show clear peaks on both p- and n-Si, but with low levels of trap concentrations (1012-1013 cm-3), and decreasing with depth from the surface. The effects of thermal oxide etching on the Si/SiO2 interface have been estimated with MOS capacitors. Negative flat-voltage shift is observed after argon plasma exposure, which removes the thermal oxide at a rate of over 100 angstrom/min at 50 V bias. C-V measurements show an order of magnitude increase in interface trap density.