We had studied the effects of hyperthermal (5.1eV) atomic oxygen (AO) on the structural characteristics of the silica layer and Si/SiOx interface formed by the oxidation of Si-single crystal by a variety of microcharacterization techniques. A laser detonation source was used to produce atomic oxygen with 5.1eV kinetic energy. High Resolution Transmission Electron Microscopy (HRTEM) and Selected Area Electron Diffraction (SAED) demonstrated that the silica layer formed on Si(100) by atomic oxygen is thicker, more homogeneous, and less amorphous, compared to the oxide layer created by molecular oxygen (MO). High spatial resolution Electron Energy Loss Spectroscopy (EELS) study confirmed that the Si/SiOx interface created by atomic oxygen is abrupt containing no suboxides as opposed to the broad interface with transitional states formed by molecular oxygen. SAED technique was used to observe sharper diffraction rings present in the diffraction pattern of Si(100) oxidized by reactive atomic oxygen as opposed to the diffused haloes present in the diffraction pattern of Si(100) oxidized by molecular oxygen. Radial Distribution Function (RDF) analyses were performed on the SAED patterns of Si(100) oxidized in atomic and molecular oxygen, indicating that a more ordered oxide is formed by atomic oxygen. Initial Fluctuation Electron Microscopy (FEM) results confirmed an increased medium range ordering in SiOx formed by atomic oxygen when compared to the non-regular arrangement present in the amorphous oxide formed by the oxidation of Si(100) in molecular oxygen.