Non-destructive optical second harmonic generation (SHG) is shown to be an effective method for detecting interfacial surface and subsurface non-visual defects in commercial thick and extremely-thin (ET) SOI wafers. A method is demonstrated for removing contributions (noise) from layer thickness variations observed in thick SOI, increasing the sensitivity and enabling detection of trace surface metal contamination. Subsurface contamination, otherwise missed by the standard flow of non-destructive characterization methods, is shown to be detected by SHG.