Raman scattering (RS) spectroscopy is a popular measurement technique that uses inelastic scattering of monochromatic light to study vibrational characteristics of a material system. A typical application of RS is for material structure determination. This paper describes the application of RS for the characterization of the preferable growth direction of well-aligned nanocrystals (NCs) deposited on sapphire substrates. The results indicate that RS could become a powerful technique for the quick determination of the NCs orientation. The redshifts and asymmetric linewidth broadening of the Raman features of RuO2 NCs are analysed by a modified spatial correlation (MSC) model, which includes the factor of stress-induced shift. The usefulness of experimental RS together with the MSC model analysis as a nondestructive structural and residual stress characterization technique for NCs has been demonstrated.