A systematic study is reported of the growth of vertically aligned few layered graphene (FLG) nanoflakes on Si (100) substrates by microwave plasma enhanced chemical vapour deposition (MPECVD) method. Asymmetric grazing incident angle X-ray diffraction (GIAXRD) studies revealed a structural transformation, from nanocrystalline graphite layers to FLG, with the increase of growth time. As the growth time increased we observed a preferred vertical orientation of FLGs accompanied by a sharp decrease in the d002 spacing. Transmission electron microscopy shows these structures have highly graphitized edge planes which terminate in a few layers (1–3) of graphene sheets. Detailed Raman studies not only support the structural transformation but also confirm that the process occurs via the sudden release of stress in nanocrystalline turbostratic graphite films. Graphical plot of all major Raman parameters (such as G peak position, ID/IG value, FWHM of D, G, and G′ peaks) vs.growth time shows a well defined trend. Using the graphical plots a tentative trajectory of the Raman parameters is proposed, which can be very useful in understanding structural transformation during growth process. Finally, a possible growth mechanism of FLGs is presented.