The development of in vitro models, which accurately recapitulate early embryonic development, is one of the fundamental challenges in stem cell research. Most of the currently employed approaches involve the culture of embryonic stem cells (ESCs) on two-dimensional (2D) surfaces. However, the monolayer nature of these cultures does not permit cells to grow and proliferate in realistic three-dimensional (3D) microenvironments, as in an early embryo. In this paper, novel 3D synthetic scaffold arrays, fabricated by two-photon polymerization photolithography, are utilized to mimic tissue-specific architecture, enabling cell-to-matrix interaction and cell-to-cell communication in vitro. Mouse ESCs (mESCs) are able to grow and proliferate on these structures and maintain their pluripotent state. Furthermore, the 3D microscaffold arrays are integrated into a microscopy slide allowing the evaluation of the expression of key pluripotency factors at the single-cell level. Comparing 2D and 3D surfaces, mESCs grown in serum+LIF on 3D microscaffolds exhibit a stronger and more homogenous expression of NANOG and OCT4 pluripotency factors, than cells cultivated in 2i media, demonstrating that 3D microscaffolds capture naive pluripotency in vitro. Thus, the slide affords a novel and unique tool to model and study mammalian early development with greater physiological relevance than conventional 2D cultures.