By combining Raman scattering and stable Ge isotopes tracing, we present a new analytical procedure to address the stability of 2D Stranski-Krastanov WL during 3D transition. Our approach is based on the experimentally verified fact that WL has no clear Raman modes and on the dependency of phonon frequencies on the isotopic composition. A direct quantification of the amount of material transferred from WL to 3D islands was achieved for Ge epitaxy on HF-etched Si(0 0 1). The estimated isotopic abundance suggests an exchange process between WL atoms and Ge atoms from direct flux during the growth of island. The influence of surface preparation on islands morphology is also investigated. We found that the growth on HF-etched Si(0 0 1) induces a low density of large dome-like islands. Carbon contaminants seem to play a critical role in self-assembling of Ge islands on hydrophobic Si(0 0 1) surface. (c) 2006 Elsevier B.V. All rights reserved.