As semiconductor manufacturing is moving towards 3 nm nodes and beyond, the development of advanced metrology techniques to control the quality of fabricated features on silicon wafers is becoming more and more crucial. Among the popular metrology methods, Scanning Electron Microscopy is one of the most important techniques since it can produce images with resolutions as low as a few nanometers. Thus, SEM is very suitable to inspect the critical dimension of nanoscale printed structures. However, CD-SEM images intrinsically contain a significant amount of background noise due to various sources. This background noise can lead to inaccurate metrology and erroneous defect detection. There is a significant requisite to reduce the noise signal in CD-SEM images while keeping the actual morphology of the pattern feature unaltered. In this paper, we proposed two deep learning-based methods to denoise SEM images, one based on (1) supervised/semi-supervised learning technique, and the other based on (2) unsupervised learning. The two proposed methods were experimented with different noisy SEM images of categorically different geometrical patterns and have demonstrated exceptional performance in reducing noise both qualitatively and quantitatively. We also have demonstrated how our proposed deep learning denoiser is applicable towards challenging application scenarios such as defect inspection and contour extraction, specifically with thin resists, with significantly improved accuracy. First, we have validated that our proposed denoising techniques, especially the unsupervised model, are effective. The unsupervised training scheme also requires single noisy acquisitions to train denoising CNNs without any ground-truth or synthetic images, against previous supervised/semi-supervised data greedy approaches. Second, the proposed deep learning denoiser assisted framework allows improved defect inspection and contour extraction with thin resists. The goal of this work is to establish a robust de-noising technique to reduce the dependency of SEM image acquisition settings and to extract repeatable and accurate CDSEM metrology information for high NA EUV. Finally, the limitations of our proposed approaches and how to overcome them were also thoroughly discussed.