Freestanding three-dimensional nanostructures have attracted intense attention for their potential application in novel electronic, optical, magnetic, biological and mechanical devices. However, controlled fabrication of highly-ordered, well-shaped and freestanding core-shell hetero-structures in large scale cost-effectively is still a challenge. Here we present the constructing of freestanding hetero-structures by taking advantages of lateral re-deposition, a phenomenon that occurred during plasma-matter interaction and usually to be minimized/avoided in conventional device fabrication. Various freestanding nanowires were irradiated under optimized conditions, in that upon etching, the sputtered species from the supporting substrates are re-deposited laterally onto the core material, mainly through plasma-phase interaction to form complex core-shell structures. Factors, including the supporting substrate, plasma power, irradiation time and gas flow rate, were used to tune the properties of the desired structures. Pencil-like, conic and wing-shape free-standing hetero-structures have been formed with controllable growth rate of sub-nanometer per minute across the width of the structure. The related mechanism was proposed. Our results indicate that such technique might be a potential approach for the fabrication of high aspect-ratio freestanding functional core-shell structures to construct mechanical, optical, biological and electrical devices.