Transmission Electron Microscopy (TEM) and scanning TEM (STEM) is widely used to acquire ultra high resolution images in different research areas. For some applications, a single TEM/STEM image does not provide enough information for analysis. One example in VLSI circuit failure analysis is the tracking of long interconnection. The capability of creating a large map of high resolution images may enable significant progress in some tasks. However, stitching TEM/STEM images in semiconductor applications is difficult and existing tools are unable to provide usable stitching results for analysis. In this paper, a novel fully automated method for stitching TEM/STEM image mosaics is proposed. The proposed method allows one to reach a global optimal configuration of each image tile so that both missing and false-positive correspondences can be tolerated. The experiment results presented in this paper show that the proposed method is robust and performs well in very challenging situations.