Comprehensive experimental and theoretical studies are reported to assess the vibrational and structural properties of 3C-SiC/Si (001) epilayers grown by chemical vapor deposition in a vertical reactor configuration. While the phonon features are evaluated using high resolution infrared reflectance (IRR) and Raman scattering spectroscopy (RSS) - the local inter-atomic structure is appraised by synchrotron radiation extended x-ray absorption fine structure (SR-EXAFS) method. Unlike others, our RSS results in the near backscattering geometry revealed markedly indistinctive longitudinal-and transverse-optical phonons in 3C-SiC epifilms of thickness d < 0.4 mu m. The estimated average value of biaxial stress is found to be an order of magnitude smaller while the strains are two-orders of magnitude lower than the lattice misfits between 3C-SiC and Si bulk crystals. Bruggeman's effective medium theory is utilized to explain the observed atypical IRR spectra in 3C-SiC/Si (001) epifilms. High density intrinsic defects present in films and/or epilayer/substrate interface are likely to be responsible for (a) releasing misfit stress/strains, (b) triggering atypical features in IRR spectra, and (c) affecting observed local structural traits in SR-EXAFS. (c) 2017 Elsevier B.V. All rights reserved.