The shape of manufactured microtubes is one of the most important properties in their numerous emerging applications areas, like drug delivery, microfluidics, and cell biology. However, making non-cylindrical microtubes with 3D features in a reproducible and single-step fashion, and meanwhile, with the ability of remote control has remained challenging. In this study, we demonstrate the controlled synthesis of highly curved 3D microtubes by two-photon polymerization with single exposure of structured optical vortices, which is generated by phase modulation with a liquid crystal spatial light modulator (SLM). We exploit the tight focusing property of the optical vortices along the light path to create 3D microtubes. By modulating the topological charge and symmetry of the optical vortices, the size and geometry of fabricated microtubes can be well controlled. Finally, we combine these two ideas with the use of magnetic nanoparticles doped resist to fabricate 3D microtubes with elaborate features and remote controllability. Precise rotation and motion of the microtubes are realized by external magnetic field. With the fabricated functional mocrotubes, elaborate capture, delivery, and realease of microparticles are demonstrated. The technology we introduce is simple, stable and achieves a high production rate to make a wide variety of functional 3D microtubes, which have broad applications in cargo transportation, drug delivery, biosensing, microfluidics, and targeted cell therapy.