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In this paper, phase field model is employed to simulate the process of femtosecond laser which irradiates on silicon surface. The numerical model is mainly used to study the micro/nano evolution process and the atomic diffusion motion of the system. Meanwhile, the Semi-Implicit Fourier spectral method and Semi-Implicit Backwards Differentiation Formula are applied for high efficiency and numerical stability. Further, the rules of surface bumps are controlled by different thermal conductivities which are systematically revealed. Our work provides a new prospect for fabricating the bumps of the probe, to obtain high sensitivity sensors in chemical and biological fields.