Stem cells have enormous potentials to both regenerate themselves and differentiate into different mature cell types, such as lung cells or liver cells. The ability to manipulate stem cell genomes is useful for both understanding stem cells at a fundamental level as well as for practical and therapeutic purposes, such as regenerative medicine. The focus of this research project is to develop a genetic tool for gene editing of human embryonic stem (hES) cells with high precision and efficiency. An engineered delivery system has been constructed and tested for their ability to deliver a genetic scissor and/or a donor DNA. We found that this system can accomplish targeted disrupt of desired genes in the genome with high efficiency (30%) and great accuracy. Our experiments also confirmed that such a system can efficiently mediate specific gene addition to a predetermined target site of hES cells. The modified hES cells maintained their self-renewal and pluripotent state of the stem cells. We have also evaluated an mRNA display technique for designing new genetic scissors specific for genome sites of stem cell interests. We showed that such a technique could be adapted to generate scaffold scissors capable of binding to target DNAs. Our experiments further demonstrated the feasibility of utilizing this powerful method to establish a library of ten trillion scissor proteins for selections to identify stem cell-specific binders.