Anhydrous HF/methanol vapor-phase chemistries were employed to etch SiO2/Si surfaces at low pressure (5-50 Torr) and ambient temperature. The oxides on Si were formed from the following: (i) RCA chemical cleaning and (ii) W-ozone treatment. Atomic force microscopy (AFM) and lateral force microscopy (LFM) were used to analyze the HF vapor-cleaned Si surfaces. AFM/LFM displayed residue islands distributed randomly upon the Si surface as a result of vapor-phase cleaning. As a result of etching RCA chemical oxides, the average lateral dimension of the residue islands is 40 nm and the average height of the islands is 6 nm. As a result of etching UV-ozone oxides, the average lateral dimension of the residue islands is 30 nm, and the average height of the islands is 3.5 nm. A decrease in residue island density is observed after the removal of a UV-ozone oxide compared to RCA chemical oxide removal. Secondary ion mass spectroscopy was used to characterize chemical impurities (O, C, F, and N) in the SiO2 films and and the Si surface after HF vapor-phase cleaning. The constituents of the residue islands have been attributed to nitrogen impurities and silicon atoms imbedded in the passivating oxides. Results indicate that condensation of methanol vapor onto the bare Si surface, after oxide removal, is necessary for residue island formation. We suggest a model in which residue island nucleation occurs from nonvolatile N-Si complexes that form hydrogen bonds with methanol molecules and diffuse into the adsorbed alcohol layer. The molecular impurities then interact and form residue islands.