The micro milling of PZT thin film deposited silicon wafer was studied with various feed rate and depth of cut. The effects on the cutting performance by the PZT thin film, tool size, and the deposited diamond thin film on the micro mill were analyzed as well. Finally, the acoustic emission (AE) signal and the cutting force collected during the cutting were analyzed for evaluating their potential in monitoring the bottom surface quality and cutting mode. The results show that the cutting characteristics of PZT thin film deposited wafer are different from the machining of the pure silicon. The less chance of ductile chip generation was obtained for the material integrated with a high percentage of PZT thin film in this study compared to the removed material integrated more part of silicon. In considering the feed rate effect on the cutting performance, the ductile mode cutting can be obtained in the test. By the way, a low feed rate range without clear chip formation during cutting was observed, and the improvement of the surface quality can be obtained with continuously lowering down the feed range. In signal analysis, the analysis of the relationship between AE signal, cutting force, and the machined quality was performed. The results demonstrate that the energy of AE signal was confirmed to increase as the quality of machined bottom surface was deteriorated. By the way, the high frequency ripple on the cutting force can also be observed when the brittle cutting mode dominates the cutting behavior.