Efficient and gentle single-cell isolation of iPSC cells is crucial to derive clonal iPSC lines as part of CRISPR-Cas9 gene-editing workflows. In this application note, we demonstrate how the Picking Platform efficiently automates the isolation and transfer of single iPSC cells into well plates for clonal outgrowth. The gentle approach of the system ensures highest cell viability and provides market-leading cloning efficiencies directly in well plates and across diverse cell substrates.