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To increase the attractiveness of the practical application of molecular sensing methods, theexperimental search for the optimal shape of silver nanostructures allowing to increase the Ramancross section by several orders of magnitude is of great interest. This paper presents a detailed study ofspatially separated plasmon-active silver nanostructures grown in SiO2/Si template pores with crystallite,dendrite, and “sunflower-like” nanostructures shapes. Nile blue and 2-mercaptobenzothiazolewere chosen as the model analytes for comparative evaluation of the Raman signal amplificationefficiency using these structures. It was discussed the features of the structures for the enhancementof Raman intensity. Finally, we showed that silver crystals, dendrites, and “sunflower-like” nanostructuresin SiO2/Si template could be used as the relevant materials for Raman signal amplification,but with different efficiency.