This paper focuses on the prognosis problem in manufacturing of the electronic chips for devices. Electronic devices are of great importance at present, which are popularly applied in daily life. The basis of supporting the electronic device is the powerful electronic chip and its manufacturing technology. Chip manufacturing has been one of the most important technologies in recent years. The etching machine is the key equipment in the etching process of the wafers in chip manufacturing. Due to the high demands for precise manufacturing, monitoring the health state and predicting the remaining useful life (RUL) of the etching system is quite important. However, the task is very hard because of the lack of knowledge of exact onset of failure or degradation and the multiple operating conditions, etc. This paper proposes a novel deep learning-based RUL prediction method for the etching system. The transformer module and random forest are integrated in the methodology to identify the health state of the machine and predict its RUL, through training with the complex data of the etching machine’s sensors and exploring its underlying features. The experiments are based on the subject of the 2018 PHM Data Challenge—for estimating time-to-failure or RUL of Ion Mill Etching Systems in an online fashion using data from multiple sensors. The results indicate the proposed method is promising for the real applications of the prognosis of the etching system for electronic devices.