Development of 3D models for drug development and disease modelling is associated with numerous challenges. Conventional methods for 3D model generation can be time consuming, resource intensive, and generate inconsistent results. Automated technologies can help to streamline complex processes to enable savings in both time and resources, while improving the robustness and consistency of workflows. The CellCelector Flex is an automated cell picking platform that provides solutions to limitations associated with conventional methods. The data presented here showcases an automated process for generation of iPSC spheroids from a single cell, resulting in the generation of a monoclonal 3D spheroid structure. Engineering monoclonal iPSC spheroids presents an opportunity to tailor models to specific diseases or conditions and provides insight into the development of 3D structures by using fluorescently labelled cell populations. Encompassing a broad portfolio of Sartorius platforms, we describe a workflow starting from single cell iPSCs through to monoclonal iPSC spheroids using live cell monitoring and endpoint phenotyping analysis.