Epitaxial Si1-xGex ultra-thin films deposited on the surface of silicon (001) using Ultra High Vacuum- Rapid Thermal Chemical Vapor Deposition (UHV-RTCVD) technique have been investigated using several nanoscale characterization techniques such as Atomic Force microscopy (AFM), Confocal Raman Spectroscopy, Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD), and EDX. Results indicate a non-planar growth surface with the formation of various nanostructures and pits. Interfacial elastic strain energy due to lattice constant mismatch is relieved through a change in the surface morphology. This is done through the formation of 3D-islands and pits on localized strain. The islands are 3-faceted truncated pyramids with the truncated face parallel to (001). In the present work we are focusing on the characterization of the Si1-xGex/Si(001) surface morphology change during growth and thermal annealing to delineate the formation mechanisms of nano-dots at the surface of such thin film material system.