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Materials with a high on-off resistance ratio could become the basis for resistive random-access memory (RRAM). It is assumed that one of RRAM types can be based on hybrid organic-inorganic systems, while particular attention is focused on hybrid systems consisting of metal nanoparticles (NP) embedded in organic matrix (OM). In this investigation we created and studied the hybrid organic-inorganic systems made of metal (Ag) nanoparticles embedded in organic semiconductor material CuPc. The LEED patterns and NEXAFS data demonstrate that the CuPc films deposited on Au(001) substrate are highly ordered and molecular planes lie parallel to the gold surface. The metal atoms were deposited on the outer surface of the organic molecular film and self-assembled into nanoparticles due to surface and bulk diffusion. The properties of nano-composite materials seem to be significantly dependent on the microstructure, i.e. the size, concentration, bulk- and size-distribution of nanoparticles; therefore we have studied by high resolution transmission electron microscopy the evolution of morphology of nano-composite films as a function of nominal metal deposition. The filled and empty electronic states of the hybrid organic-inorganic systems, energy level alignment at interfaces formed between metal nanoparticles and the organic semiconductor CuPc as well as the chemical interaction at the NP/OM interface were studied by UPS, XPS and NEXAFS methods.