The present work puts forward a generalized simulation model to evaluate the topography of ball-end milled surfaces by considering both the tool deflection and the tool runout. Firstly, a solid ball-end mill with S-shaped cutting edges is modeled as the basis. Then the tool tip trajectory is derived from the tool runout as well as the cutting forces induced tool deflection. And consequently the topography and scallop height of the machined surface are estimated by the numerical calculations of the matrix equations. With good expandibility, the proposed model can incorporate more machining information such as the movements of rotatory axes and tool wear, and hence, can be used to optimize the cutting conditions and parameters in 5-axis ball-end milling process.