Metal-filled carbon nanotubes (CNTs) are known to be used as pen-tip injectors for 3D manufacturing on the nanoscale. However, the CNT interior cannot accumulate enough material to fabricate complex metallic nanostructures. Therefore a method for refilling the CNT cartridge needs to be developed. The strategy for refilling of CNT cartridges is suggested in this study. Controlled growth of gold nanowires in the interior of isolated CNTs using a real-time manipulator installed in a transmission electron microscope is reported herein. The encapsulation process of discrete gold nanoparticles in the hollow spaces of open-ended multi-wall CNTs was evaluated in detail. The experimental results reveal that the serial loading of isolated gold nanoparticles allows the control of the length of the loaded nanowires with nanometer accuracy. Thermophoresis and the coalescence of gold nanoparticles are assumed to be the primary mechanisms responsible for gold loading into a CNT cartridge.