The global demand for air travel and air transport is expected to increase again in the next couple of years and so the environmental protection will also increasingly come into focus again. In the aviation sector, this means not only saving fuel and reducing emissions but also reducing the noise pollution caused by aircrafts. A typical method for noise reduction is the use of acoustic liners for sound insulation. Among different designs, acoustic liners can consist of sandwich panels, with one perforated, micro-drilled skin layer, a honeycomb structure and a closed rear layer. Wherever the operating conditions allow, the skin layers are made of carbon fiber reinforced plastics (CFRP), due to weight reasons. Compared to conventional drilling methods for CFRP, laser drilling offers unique benefits such as significantly smaller achievable bore diameters, wear free cutting and flexibility in bore diameter. However, for a large-scale application of laser micro drilling, the process efficiency must be increased and a process control is necessary to avoid damage due to excessive heat input. In this investigation, a process control method based on thermography is presented and evaluated. The control mechanism uses the temperature course in the drilling area to decide whether the process can be terminated in order to avoid time losses and unnecessary heat input. This method was found to be very reliable, however, the synchronization between temperature recording and laser irradiation and the data interpretation need further improvement.