AbstractTwo-dimensional (2D) crystals are attracting growing interest in various research fields such as engineering, physics, chemistry, pharmacy, and biology owing to their low dimensionality and dramatic change of properties compared to the bulk counter parts. Among the various techniques used to manufacture 2D crystals, mechanical exfoliation has been essential to practical applications and fundamental research. However, mechanically exfoliated crystals on substrates contain relatively thick flakes that must be found and removed manually, limiting high-throughput manufacturing of atomic 2D crystals and van der Waals heterostructures. Here, we present a deep-learning-based method to segment and identify the thickness of atomic layer flakes from optical microscopy images. Through carefully designing a neural network based on U-Net, we found that our neural network based on U-net trained only with the data based on realistically small number of images successfully distinguish monolayer and bilayer MoS₂ and graphene with a success rate of 70–80%, which is a practical value in the first screening process for choosing monolayer and bilayer flakes of all flakes on substrates without human eye. The remarkable results highlight the possibility that a large fraction of manual laboratory work can be replaced by AI-based systems, boosting productivity.