Embedded Si nanocrystals in SiO2 have a large current interest due to the prospects for practical applications. For most of these it is essential to characterize and ultimately control the nanocrystal size, size distribution and spatial distribution. Here we present a study of Si nanocrystals and clusters in SiO2 studied by atomic force microscopy (AFM). Since it is an indirect method, it requires several other methods to establish a reliable description of the structure of the samples. We here compare the AFM results with photo luminescence (PL) and transmission electron microscopy (TEM). Si nanocrystals in thermal oxide films (similar to 250 nm) were fabricated by 100 keV Si ion implantation at a dose of 1 x 10(17) cm(-2) followed by high temperature annealing. AIM micrographs were taken after different etching times of the oxide and compared to TEM measuerements of the nanocrystal size and distribution. The correlations observed strongly indicate AIM signatures connected to the nanocrystals. We have analyzed and modeled the etch sectioning technique. Comparisons with the experiments let us conclude that the sectioning technique has some memory effect, but yields a distribution of nanocrystals with depth. A dose of 5 x 10(16) cm(-2) yields a PL blue shift of about 100 nm relative to the higher dose. No nanocrystals are observed with TEM in this latter case. However distinct signatures can be observed with AFM and is tentatively attributed to the presence of non-crystalline Si-rich nanoclusters. (C) 2006 Elsevier B.V. All rights reserved.