The design of reliable and secure codes with finite block length is an important requirement for industrial machine type communications. In this work, we develop an autoencoder for the multi-mode fiber wiretap channel taking into account the error performance at the legitimate receiver and the information leakage at potential eavesdroppers. The estimate of the mutual information leakage includes AWGN and fading channels. The code design is tailored to the specific channel setup where the eavesdropper experiences a mode dependent loss. Numerical simulations illustrate the performance and show a Pareto improvement of the proposed scheme compared to the state-of-the-art polar wiretap codes.