Embryonic and induced pluripotent stem cells (iPSC), have the capacity for prolonged self-renewal and differentiation into numerous distinct cell lineages. Human pluripotent stem cells (hPSC), therefore, may be a reliable source of donor cells for transplantation therapies and for drug screening. These applications require tight control over the in vitro culture microenvironment to obtain desired hPSC differentiated derivatives with high efficiency and functional quality. Microscale high-throughput culture systems are useful tools for mimicking and controlling hPSCs in vivo-like microenvironment unveiling the complex interactions between cell-cell and cell-soluble/immobilized factors. We have established a robust and reproducible 3D microarray platform for expansion and differentiation of hiPSCs into neural progenitors, ultimately enabling the analytical quantification of the effects of growth factors and small molecules that impact cell viability and phenotypic characteristics. This platform also enables high-throughput studies to be performed on the toxicity of small molecules towards hiPSC-differentiated derivatives and evaluate different cellular sensitivities to drugs, drug candidates, chemicals and other small molecules.