In Complementary Metal-Oxide Semiconductor (CMOS) technology, scaling down has been a key strategy to improve chip performance and reduce power losses. However, challenges such as sub-threshold leakage and gate leakage, resulting from short-channel effects, contribute to an increase in distributed static power. Two-dimensional transition metal dichalcogenides (2D TMDs) emerge as potential solutions, serving as channel materials with steep sub-threshold swings and lower power consumption. However, the production and development of these 2-dimensional materials require some time-consuming tasks. In order to employ them in different fields, including chip technology, it is crucial to ensure that their production meets the required standards of quality and uniformity; in this context, deep learning techniques show significant potential. This research introduces a transfer learning-based deep convolutional neural network (CNN) to classify chemical vapor deposition (CVD) grown molybdenum disulfide (MoS2) flakes based on their uniformity or the occurrence of defects affecting electronic properties. Acquiring and labeling a sufficient number of microscope images for CNN training may not be realistic. To address this challenge, artificial images were generated using Fresnel equations to pre-train the CNN. Subsequently, accuracy was improved through fine-tuning with a limited set of real images. The proposed transfer learning-based CNN method significantly improved all measurement metrics with respect to the ordinary CNNs. The initial CNN, trained with limited data and without transfer learning, achieved 68% average accuracy for binary classification. Through transfer learning and artificial images, the same CNN achieved 85% average accuracy, demonstrating an average increase of approximately 17%. While this study specifically focuses on MoS2 structures, the same methodology can be extended to other 2-dimensional materials by simply incorporating their specific parameters when generating artificial images.