An electrochemical technique for the fabrication of intermediate nano-sized pores in silicon (50–200) nm in aqueous HF solution is reported. Attempts to achieve similar nano-sized pores in the presence of organic solvents are also presented. Mesopore formation beginning with pore sizes <50 nm followed by pore widening in alkaline etch solution is also attempted. The desired pore size is obtained with a KMnO4 oxidizing agent in the presence of surfactant. Our findings reveal that the applied current density during the fabrication process is a decisive factor. The concentration of HF and KMnO4 should be controlled within appropriate ranges. A multilayer with two different pore morphologies is fabricated on the same substrate using the same electrolyte simply by changing the applied anodic current. Application of such cylindrical pore arrays as templates for polymer nanofabrication is demonstrated. By selective dissolution of the silicon membranes, we successfully obtained nanowires of polypyrrole (PPy) with ∼100 nm diameter size. The fabrication process, the electrochemical measurements, the formation mechanism and the different pore morphologies are investigated in detail.