Micro milling is a flexible and economical method to fabricate micro components with three-dimensional geometry features over a wide range of engineering materials. But the surface roughness and micro topography always limit the performance of the machined micro components. This paper presents a surface generation simulation in micro end milling considering both axial and radial tool runout. Firstly, a surface generation model is established based on the geometry of micro milling cutter. Secondly, the influence of the runout in axial and radial directions on the surface generation are investigated and the surface roughness prediction is realized. It is found that the axial runout has a significant influence on the surface topography generation. Furthermore, the influence of axial runout on the surface micro topography was studied quantitatively, and a critical axial runout is given for variable feed per tooth to generate specific surface topography. Finally, the proposed model is validated by means of experiments and a good correlation is obtained. The proposed surface generation model offers a basis for designing and optimizing surface parameters of functional machined surfaces.