The size influence of 3D silver nanoparticle aggregates on surface-enhanced Raman scattering (SERS) is investigated. Micrometer and nanometer sized wells prepared on a polydimethylsiloxane (PDMS) surfaces are filled with cetyltrimethylammonium bromide (CTAB)-coated silver nanoparticles. A concentration of CTAB around its critical micelle concenteration is used not only to form a bilayerlike structure around the nanoparticles and thus generate nanometer-sized gaps in the aggregates, but also to improve the compartibility of the surface charge, properties of the silver nanoparticles with the surface of PDMS and thus successfully fill the wells by assembly of silver nanoparticles into 3D structures. A resonance-free enhancement factor of 10(7) can be easily achieved on larger aggregates and the enhancement factor increases with decreasing size of the 3D aggregates which is contrary to reported studies on conventional silver clusters. We find that the number of silver nanoparticles in the 3D aggregate should be less than 200-300 for optimal SERS performance.