In this paper, fractal reconstruction of rough membrane surface with a modified Weierstrass-Mandelbrot (WM) function was conducted. The topography of rough membrane surface was measured by an atomic force microscopy (AFM), and the results showed that the membrane surface was isotropous. Accordingly, the fractal dimension and roughness of membrane surface were calculated by the power spectrum method. The rough membrane surface was reconstructed on the MATLAB platform with the parameter values acquired from raw AFM data. The reconstructed membrane was much similar to the real membrane morphology measured by AFM. The parameters (including average roughness and root mean square (RMS) roughness) associated with membrane morphology for the model and real membrane were calculated, and a good match of roughness parameters between the reconstructed surface and real membrane was found, indicating the feasibility of the new developed method. The reconstructed membrane surface can be potentially used for interaction energy evaluation.