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The rectangular microtubes array of perchlorinated copper phthalocyanines (Cl16CuPc), were synthesized by physical vapor deposition technique without using any template or catalyst. The synthesis process of the tubular structure is very simple, easy to control, and a little raw material is used. The morphology and crystal structure of the obtained samples were analyzed by means of scanning and transmission electron microscopy (SEM and TEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy (XPS). The microtubes have an entire hollow interior, open ends with rectangular cross-section, a large interior of 1.4-1.8μm width, and the thin walls of 80-100 nm. The obtained products exhibit excellent crystalline nature, high chemical and thermo-dynamic stability, excellent biocompatibility, as well as innocuity. It is believed that these well-defined microtubular structures of an organic material will be used as active materials for solar cells, nanodevices for field emission apparatus, microchannels for biochip and microvessel for drug delivery.