A wrapped alignment mark structure is proposed for a nano-fabrication process by e-beam lithography (EBL) with organometallic vapor phase epitaxy regrowth. To protect the alignment marks during regrowth, a SiO2 layer covers the surface of the gold mark and a thin tungsten layer is inserted between the mark and the substrate. The waveform serving as a mark detection signal is not significantly reduced after regrowth. By employing this mark system in EBL, an aligned nanostructure with a buried double-slit heterostructure and fine multi-electrodes is fabricated successfully to show the feasibility of this alignment mark method of wrapping. The center to center spacings of the double-slit and the fine electrodes are 40 nm and 50 nm, respectively.