After a few unfortunate experiences with the regular transformative Witness Protection Program, where people made choices they weren't entirely prepared to live with, the Bureau have developed a new method for selecting and creating new identities: connecting the minds of the participants to an advanced AI through a new VR system, and letting the AI calculate and design a set of new identities for the clients.
While technically complicated, the process itself is pretty simple. It allows multiple people who are to be placed into Witness Protection together, and then create a set of identities that fit together, taking into consideration everyone's wants and desires.
Of course, to do this the program needs access to the subconscious of the participants. This is done by giving everyone a small dose of a psychoactive drug, allowing them to more freely associate and float towards the options that fit them. Then everyone's released into the VR system, where they're presented with an almost infinite myriad of fluid bodies of all ages, genders, sizes, races, and even in some cases species. As the process goes on, and the AI gets an understanding of the desires and curiosities of the participants, it'll start eliminating options, the remaining options shifting subtly to fit each other better. If a trio drifts towards a male and a female of similar ages, and a female significantly younger than the other two, it might subtly shift the psychology of the man and the woman so that they'd fit well together as a couple, and make the younger female into someone who could be their daughter. A participants desires, say to have a child, may also influence the options available for the other participants...
Once the process is over, the identities and relationships crystallized, the next step begins. The participants will be put into a deep, sleep-like trance, and while their bodies are transformed on a genetic level, subliminal conditioning and hypnotic suggestions are implanted, allowing every participant to learn what they need to know about their new lives, and acquire the skills required to live the life. The process can even "lock off" skills and knowledge the participant already has, sealing it away so that, while not entirely impossible to access, it won't come natural.