An important design approach for sensitive and robust surface enhanced Raman scattering (SERS) substrates is the use of metal nanoparticle aggregates with nanometer tailored interstitial distances between their surfaces, in order to confine the electromagnetic energy. The nanostructural instability of the aggregates to agglomeration due to their strong van der Waals force poses a challenge for the preparation of large-scale, reliable SERS substrates. We present a novel route for preparing stable and highly active SERS substrates using polymer-metal fractal nanocomposites. This methodology is based on the unique morphology of fractal nanocomposite structures formed just below the percolation threshold that consists of extremely narrow (approximately 0.8 nm) interstitial polymer junctions between the Ag nanoparticle aggregates along with the appropriate nanoscale (<100 nm) surface roughness. Such nanomorphology allows the formation of well-defined and large numbers of hot spots where the localization of electromagnetic energy can result in very large enhancement of the Raman signal. We applied a simple plasma etching process to remove the polymer structures that allowed the formation of Ag structures with very uniform and controllable inter-particle gaps that were proved to provide significant SERS enhancement of typical biological systems such as double-stranded deoxyribonucleic acid (dsDNA). These advanced nanocomposite films could be used for the development of large-scale spectroscopy-based sensors for direct detection and analysis of various biological and chemical samples.