The authors would like also to thank Jos?? Santos for technical support. ; In this work, SiGe/SiO2 multi-layer (ML) films with layer thickness in the range of a few nanometers were successfully fabricated by conventional RF-magnetron sputtering at 350??C. The influence of the annealing treatment on SiGe nanocrystals (NCs) formation and crystalline properties were investigated by Raman spectroscopy and grazing incidence x-ray diffraction. At the annealing temperature of 800 ??C, where well defined SiGe NCs were observed, a thorough structural investigation of the whole ML structure has been undertaken by Rutherford backscattering spectroscopy, grazing incidence small angle x-ray scattering, high resolution transmission electron microscopy, and annular dark field scanning transmission electron microscopy. Our results show that the onset of local modifications to the ML composition takes place at this temperature for annealing times of the order of a few tens of minutes with the formation of defective regions in the upper portion of the ML structure. Only the very first layers over the Si substrate appear immune to this problem. This finding has been exploited for the fabrication of a defect free metal-oxide-semiconductor structure with a well-defined single layer of SiGe NCs. A memory effect attributed to the presence of the SiGe NCs has been demonstrated by high frequency capacitance-voltage measurements. ; FEDER funds through the COMPETE program ???Programa Operacional Factores de Competitividade??? and by Portuguese funds through Portuguese Foundation for Science and Technology (FCT) in the frame of the Project PTDC/FIS/70194/2006 ; the transnational access framework of the ANNA Eu Project (Contract No. 026134 RII3) through the funding of the ANNA_TA_UC9_RP006 proposal ; ELETTRA Synchrotron Radiation Center for the measurements at the SAXS beamline funding received from the European Community???s Seventh Framework Programme (FP7/2007???2013) under Grant Agreement No. 226716 ; Scientific and Technological Cooperation Program between Portugal (FCT) and Morocco (CNRST)-2010/2011 ; European COST MP0901-NanoTP Action. ; FCT grant: SFRH/BD/45410/2008 ; FCT grant: SFRH/BPD/64850/2009 ; FCT grant: SFRH/BPD/26532/2006 ; I.C. acknowledges support from the Unity through Knowledge Fund. ; M.B. acknowledges support from the Ministry of Science Education and Sports, Republic Croatia (Project No. 098-0982886-2866).