For the second time, Jesus moves “a little way off” to pray to the Father. This prayer is not for instruction, but of gratefulness for the faith of the twelve, as well as those who were gathered. The previous experience describing whiteness (verse 25 in this chapter) indicated that the apostles had been purified, and that is how Jesus speaks of them. He expresses thanks “that [the Father has] purified those whom [He, Jesus, has] chosen.
In verse 29, Jesus says: “I pray not for the world, but for those whom thou hast given me out of the world, because of their faith, that they may be purified in me, that I may be in them as thou, Father, art in me, that we may be one, that I may be glorified in them.” This is a recognition that not all who are in the world will be capable of receiving the purification Jesus spoke of. Nevertheless, Jesus prays for those who do have the ability to understand, keep the commandments, and become purified. When he says that “they may be purified in me, that I may be in them as thou, Father, art in me,” it is a reference to their ultimate exaltation, their presence in the Celestial Kingdom.