The implementation of Quantum Dots (QDs) in devices allows novel electronic and opto-electronic functions. Strain driven Stranski-Krastanov growth mode enables the formation of nanometric islands (on wetting layer) whose density and geometry depend on growth conditions (temperature, rate) and surface structure (cleaning). The island positions are random. However, they can be influenced by surface patterning. In this work, the MBE growth of self-organized Ge QD structures in oxide windows is investigated. The studied Ge QD structures are composed by either a single Ge layer directly grown on a Si substrate, or double layer formed by a Ge QD layer on top of a Si buffer layer. Different surface preparation (dry etching with and without anisotropic wet etching) and cleaning (HF dip or RCA cleaning) schemes have been used. It is found that the cleaning and the Si buffer layer growth have strong influence on island nucleation. Preferred nucleation at the window edge and/or nucleation at the window center is observed under certain conditions. Interestingly, negligible influence (this is needed for most device works) is found only if Ge is grown directly on the RCA cleaned window.