Total oxide thickness and molar volume ratio for scanned probe microscopy (SPM) oxide nanostructures are obtained for a wide range of silicon substrates and exposure conditions by high-resolution cross-sectional transmission electron microscopy (HR XTEM) and atomic force microscopy (AFM). Oxide density is shown to be a function of substrate doping and voltage pulse parameters. Dislocations produced by the SPM voltage pulse within the silicon substrate are reported from direct XTEM observation for the first time. These dislocations are completely annealed out at 600 degrees C. The dimensional response of SPM oxides to annealing and/or mechanical stress imposed by metal deposition are found to be negligible for n-type substrates, but SPM oxide films on p-type substrates are strongly compressed or expanded. This behavior is attributed to the formation of positively charged defects and ionic/electronic recombination near the growing Si/SiOx interface. Implications of these results for use of SPM oxide in silicon nanodevice processing are discussed.