In conventional machining, cutting conditions such as cutting speed, feed rate, and depth of the cut have great influence on the surface roughness. In micro machining, however, the surface shape is affected by not only the machining parameters mentioned earlier but also tool stiffness, system stability, and workpiece properties caused by the miniatured structure and cutting tool. Especially, in a micro-machine system, the difference between the cutting forces in the recursive cuts introduces the vibration easily. A high spindle causes instability of the system, increases the temperature in the cutting process, and also changes the tool’s shape. This study introduces a method to predict the surface shape of the workpiece based on the machining conditions in micro milling. The micro-milled surfaces in different machining conditions are predicted by a computer simulation including the vibration model and the simulated results show good agreement with the experimental results.