A three-dimensional dynamic model for nano/micro-fabrications of silicon was presented. With the developed model, the fabrication process of silicon on nothing (SON) structure was quantitatively investigated. We employ a diffuse interface model that incorporates the mechanism of surface diffusion. The mechanism of the fabrication is systematically integrated for high reliability of computational analysis. A semi-implicit Fourier spectral scheme is applied for high efficiency and numerical stability. Moreover, the theoretical analysis provides the guidance that is ordered by the fundamental geometrical design parameters to guide different fabrications of SON structures. The performed simulations suggest a substantial potential of the presented model for a reliable design technology of nano/micro-fabrications.