In this paper we demonstrate a novel complex array structure comprising well-aligned Au nano-rods (10 nm in diameter) encapsulated inside 15nm radius multiwalled carbon nanotubes (MWCNTs). A pre-aligned and open-ended nano-porous MWCNT membrane is used as the starting material. Au nano-rods are precisely deposited and aligned inside the hollow channels of CNTs by inter-diffusing HAuCl4 precursor and the reductant solution. Ultra-long Au nano-wires and spherical Au nano particles are also observed in the CNT cavity with the same diameter in special case. By using high-resolution TEM(HRTEM), Scanning transmission electron microscopy(STEM), 3-demensional TEM(3D-TEM) and Energy dispersive X-ray spectroscopy(EDX), the precious location and composition of the encapsulated Au components with various structures are confirmed. This aligned Au@CNT endohedral material has important potential applications in nano-catalysis, waveguides, as well as novel plasmonic devices.