Let us first address a clearly delineated case:
There is a law that when urinating in the middle of a meal and using only one hand to clean oneself, one need only wash that hand - Yoma 30a, Shul'han Arukh Ora'h 'Haim 170:1. No differentiation was made regarding the fingers used, so I would assume that in a meal it would be required to still wash the whole hand. So it is clear that you don't need to wash both hands.
Now regarding prayer:
Nevertheless for praying as opposed to eating, since the requirement to wash one's hands fully besides once in the morning in order to pray (according to the opinion accepted as halacha) is not restrictive, and only their cleanliness is (ibid. 92:6), despite that a-priori halacha requires washing the whole hand (ibid. 92:5), nevertheless once already in the middle of prayer that one can't move in, an act of cleaning alone is enough. Therefore when in the middle of the "Amidah" it would seem that it would be enough to clean the finger (since we are only concerned with cleanliness and cleaning a clean part of the hand does nothing, as it is already clean). When in a part of prayer that permits walking around, one would have to wash the whole hand (Mishna Berura 92:27) since a priori, more than just "cleaning" is required - "washing".
Of course one should not touch the dirty area of the body when in prayer (ram"a 92:7).