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The targeted scientific breakthrough is a study of controlled self-organized process of nanosized structures based on porous silica or alumina on silicon surface systems where dielectric pores are selectively filled by plasmonic metals (silver and gold) for a formation of dimensionally divided plasmonic nanostructures. Swift heavy ion track technology was used for the pre-patterning of porous surfaces with nanoscaled metal particles. Wet-chemical methods of the deposition of noble metals and their combinations in the pores was applied for the formation of the plasmonic nanostructures. The characterization of plasmonic structures was carried out by surface analytic methods like SEM, EDX, EBSD, TEM, etc., which are combined with theoretical modeling of growth processes and plasmonic properties supporting the optimization process of the surface. The Raman scattering measurements were performed at room temperature on a Witec or Horiba based Raman setup (532 nm and 633 nm laser) using Ellman’s reagent or bilirubin. The spatially separated plasmonic nanostructures have been synthesized using heavy ion track technology and self-organization of metal atoms in the closed volumes. The first pre-tests of these nanostructures in Raman scattering spectroscopy have been performed. The first data indicates the possibility of detecting ultra-small concentrations of the Ellman’s reagent on silver dendritic nanostructures, the detection limit of 10-15 M was achieved that corresponds that Raman signal enhanced above 13 orders of magnitude. The detecting ultra-small concentrations of the Bilirubin on gold nanostructures, the detection limit of 10-9 M, was achieved. The foregoing allows us to conclude that spatially separated plasmonic nanostructures in the pores of the SiO2 template on silicon are a new promising effective plasmon active surfaces for SERS, which are of record high sensitivity and can find application in chemo- and biosensorics.