Drilling a stack made of carbon fiber-reinforced plastic (CFRP) material and aluminum or titanium, which is typical in the aircraft industry, is investigated for improved performance and economy. Using the same drill under the same process parameters to make holes in both materials requires compromising the quality of the holes and the drilling performance in the CFRP or in the metal layer. One way to overcome this need to compromise is to change the process parameters during drilling and to use the most suitable parameters for each material. This is possible when the thickness of each layer is known. This is not the case with large airplane parts with changing profiles in which the thickness of the different material layers varies along the profile. The current investigation presents a method based on an acoustic emission signal for identifying the transition point between materials and the point of entrance and exit from each material during the drilling process. Finding those points from the acoustic emission signal in real time was achieved by applying a novel pattern analysis algorithm using real drilling tests results. The proposed method can be used to change the process parameters and correctly adapt them to the material being drilled. Two types of drills were used in the experiments, a standard carbide drill and a carbide stepped drill. In both cases the proposed method showed good results, although using a stepped drill allows more time to make changes in the process parameters.