Non-integrating episomal vectors have become an important tool for induced pluripotent stem cell (iPS) reprogramming. The episomal vectors carrying the Yamanaka reprogramming factors (Oct4, Sox2, Klf, and Myc) function similarly to retrovirus or lentiviral constructs, yet they are lost through cell division, resulting in pluripotent stem cells that maintain an unmodified genetic background. Given that induction of pluripotency is a highly stochastic process, tight regulation of reprogramming factor dosage, such as those available in viral systems may allow for more efficient generation of higher quality iPSCs. We present a modified set of vectors that express separable fluorescent proteins to allow for enrichment of transfected cells, and control of reprogramming factor copy number and relative dosage.