The echo traces in the ionograms contain key information about the ionosphere. Therefore, the accurate extraction of these traces is crucial for the subsequent work. This paper transforms the original signal processing problem into a semantic segmentation task, combines it with the currently popular deep learning techniques, and proposes a multiscale Transformer network to achieve pixel-level trace extraction. To train the proposed model, we built a dataset by discretizing the original echo data, labeling, and other preprocessing work. A series of advanced semantic segmentation networks are utilized for comparative experiments. The analysis of the results indicates that the proposed network excels in performance, achieving the highest scores on key semantic segmentation evaluation metrics, including mIoU, Kappa, Dice, and AUC-ROC. In addition, this paper also designs a series of ablation experiments to observe the changes in network performance and to evaluate the rationality of the network design. The experimental results demonstrate the effectiveness of the network in the trace extraction task, which plays a positive role in the subsequent electron density reversal work.