Aniline is electropolymerized through mesoporous silica nanopores (100 nm-long, 3 nm in diameter) orthogonally oriented on indium-tin oxide (ITO). Only a few polyaniline (PANI) wires are accommodated in the nanochannels and their growth is electrochemically controlled. The electronic transport properties of PANI@SiO2 are studied by Conductive Atomic Force Microscopy (C-AFM), using a Pt-coated C-AFM tip as a top electrode to complete ITO/PANI@SiO2/Pt molecular junctions (MJs). Three different behaviors are observed. First, linear I/V curves are obtained when PANI is deposited in the nanopores with material spilling over the silica membrane. Transport occurs through many PANI@SiO2 channels where the overall conductance is high. Second, flat I/V curves are recorded, indicating "insulator" behavior when the SiO2 nanopores are not fully filled by PANI wires. Thirdly, non-linear I/V curves, which are quantitatively highly reproducible and independent of the area probed, are obtained. These are attributed to the formation of MJs where the C-AFM tip in contact with nanopores acts as the top electrode with vertical PANI wires just filling the SiO2 channels.