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Raman and atomic force microscopy (AFM) mapping on the same selected area are used to get unique information about the morphology of Si nanocrystals (NCs) embedded in SiO 2 , which is difficult to obtain by any other conventional technique. The sensitivity of Raman spectroscopy to surface/interface and confinement effects in NCs is effectively used to correlate the Raman intensity profile in Raman mapping with the topography obtained from AFM to understand that Si NCs are clustered in i) smaller clusters (∼100 nm) organized closely in two dimensions (2D) and ii) big (∼2 μm) three dimensional (3D) isolated clusters, although the growth is carried out to be multilayer (Si/SiO 2 ). Raman mapping performed by varying the focal spot along the depth shows stacking of larger (>∼60 Å) to smaller sizes (<∼40 Å) Si NCs from bottom to top for some clusters. To understand the observed morphologies, further study of specially grown Si–SiO 2 nanocomposites is performed, which suggest formation of smaller Si NCs at the top due to annealing at 800 °C in Si rich SiO 2 and possible existence of thermal gradient in an insulating matrix of SiO 2. Larger Si NCs are formed in the laser induced plume (plasma) itself. [ABSTRACT FROM AUTHOR]