The authors present a novel in-situ method of fabricating crystalline gold nanoparticles by self-organization. This nanoparticles are grown and modified in a surrounding thin film matrix using two different host materials (YBa2Cu3O7-δ and SrTiO3) prepared by a pulsed laser deposition technique. The crystalline Au nanoparticles are formed out of a gold seed layer whereby the thickness of the initial seed layer influences the particle size and their distribution density. As we will show, using a matrix based preparation technique offers several advantages over conventional preparation methods. On the one hand, nanoparticle size and the distribution density can be controlled individually. On the other hand, by choosing an appropriate matrix material as well as suitable growth conditions also the shape of the resulting particles can be modified. Thus, also anisotropic nanoparticles can be prepared without using highly sophisticated methods like electron beam lithography or focused ion beam techniques. As one might have to extract the nanoparticles or at least theirs tips from the surrounding matrix material to realize photonic applications, we will show that an extraction is easily possible by selectively etching the matrix. This extraction process does not influence the particle distribution, i.e. particles can be prepared and extracted at distinct positions on the substrate utilizing a patterning of the Au seed layer. A spectral characterization of extracted as well as embedded particles will be presented based on microspectroscopy as well as on measurements using an integrating sphere.