Finish milling with a ball end mill is a key process in manufacturing high-precision and complex workpieces, such as dies and molds. Because of the complexity of the milling process, it is difficult to evaluate the microcharacteristics of machined surfaces real time, which necessitates the simulation of the process. In this area, the existing related simulation researches mainly focus on scallop height evaluation, but few have presented a whole picture of the microcharacteristics of milled surfaces. This paper develops a comprehensive simulation system based on a Z-map model for predicting surface topographic features and roughness formed in the finish milling process and studies the effect of machining parameters. The adoption of the discretization concept of the tool’s cutting motion makes it possible to dynamically track the cutting tool-workpiece interaction with the tool movement and to describe the cutting edges-workpiece discrete cutting interaction more realistically and, therefore, the microcharacteristics of the machined surfaces more accurately. Also, the effects of the cutting tool run-out and wear are incorporated into the developed model through modifying the tool center motion and the cutting-edge shape, respectively. As a fundamental study, the tool-swept envelope has been simulated. The developed simulation system is applied to thoroughly study the surface features formed by the 2.5-axis finish milling process. The application for general three-axis machining is discussed. Additionally, this paper studies the effect of the tool inclination, which is the most common characteristic in 3+2- or five-axis milling processes, on the machined surface features. Experiments are carried out to study the milling process and to verify the simulation results. The difference between the simulated and experimental results is discussed, and the reason behind the difference is explored.