Si nanocrystals in thermal oxide films ( similar to 250 nm) were fabricated by 100 keV Si ion implantation at various doses followed by high temperature annealing. After annealing a sample implanted with a dose of 1 x 10(17) cm(-2) at 1050 degrees C for 2 h, a broad photoluminescence peak centred around 880 nm was observed. A dose of 5 x 10(16) cm(-2) yields a considerable blue shift of about 100 nm relative to the higher dose. Transmission electron microscopy and atomic force microscopy (AFM) are used to characterize the microstructures in the SiO2 film. The limitations of these techniques for the study of the nanostructures are addressed in this paper and it is suggested that AFM combined with etching can yield a structural spectroscopy with very good sensitivity.