We report on improved electrical conductivity in poly(3-hexylthiophene) (P3HT)/2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4-TCNQ) composite nanowires grown using an anodized aluminum oxide (AAO) template. The electrical conductivity of individual nanowire measured by four-probe scanning tunneling microscopy shows that F4-TCNQ molecules are effectively doped into P3HT by capillary force. The resistivity is tuned in the 0.1-10 Ω cm range by changing the F4-TCNQ concentration from 10 to 0.1 wt % and is 2-4 orders of magnitude smaller than that of the corresponding P3HT/F4-TNCQ thin film composites. The AAO template-assisted synthesis approach thus appears to be effective for high chemical doping and for improving the electrical conductivity of the molecular wires.