Regenerative medicine uses cell alone or in combination with carrier to deliver at the required site for restoring the normal functions of diseased or degenerated tissue. Various strategies to restore tissue functions involve specific cell types, scaffolds and delivery processes that are still in developmental stage. Obtaining sufficient quantity of cells by non-invasive approach for the application in regenerative medicine is still a challenge. Pluripotent stem cells (PSCs), including embryonic stem cells and induced pluripotent stem cells (iPSCs), possess the inherent ability of self-renewal and differentiation into many cell types. In particular, iPSCs are of a special interest because patient-derived iPSCs have the ability to reproduce patient-specific clinical conditions. The development of manufacturing systems for PSCs, including cell culture engineering, is a challenging research field for the clinical application of PSCs such as in regenerative medicine. One of these manufacturing systems uses magnetic nanoparticles which are well known for their application in magnetic resonance imaging and magnetic hyperthermia. Besides, this chapter is focused on the basics of magnetic nanoparticles, its functionalization and further applications of a magnetic force-based cell manufacturing system for pluripotent stem cells. Indeed, we have developed a procedure in which cells are labeled with magnetite cationic liposomes via electrostatic interaction between the positively charged liposomes and the target cells. The culture system may provide a useful tool for studying the behavior of PSCs and an efficient way of PSCs manufacturing for clinical applications.