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Nanostructured silicon thin films prepared by layer-by-layer deposition technique were studied. The films were grown at different deposition conditions such as radio-frequency (rf) power, hydrogen to silane flow-rate ratio and substrate temperature. The effect of these deposition conditions on the surface morphology, hydrogen bonding property and crystallinity of the films were studied. These properties were investigated using field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FTIR), micro-Raman spectroscopy and X-ray diffraction (XRD). The results showed various morphological features of nanostructured silicon thin films which consist of clusters of nanocrystallites surrounded by grain boundaries. Raman results showed the presence of crystalline phase in these films which was contributed by the nanocrystallites. FTIR results demonstrated presence of Si-H2 bonds which we believe were present in the grain boundaries separating the nanocrystallites from each other in the clusters and also Si-H bonds which were present in the amorphous phase separating the clusters.