Si (100) with and without a 14–25 Å14–25Å thick native oxide was laser machined at grazing incidence using a Ti:sapphire femtosecond pulsed laser under ultrahigh vacuum conditions. The resulting damage feature size and morphology indicate that the presence or absence of the native oxide significantly affects the mechanism for femtosecond laser-induced damage. We propose that a fluence-dependent modification of the oxide by the incident laser pulse must be considered when studying femtosecond laser damage of Si (100) with a native oxide. Data are also presented that are consistent with a dose-dependent phase transformation in the amorphous oxide. The implications of the native oxide, including relative damage thresholds of the underlying Si (100) and the role of the oxide in damage morphology are addressed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87851/2/264103_1.pd