If a woman does wudoo’ then puts makeup on her face, that does not matter, and it does not affect her wudoo’ or her prayer, so long as it is not naajis, because purity of clothes and body are essential for the prayer to be valid.
It should be noted that it is not permissible for a woman to wear makeup in front of non-mahram men, because she is commanded to cover her face in front of them and because wearing makeup is an adornment that leads to fitnah. If she does that and then prays, she will have the reward for her prayer but she will have the burden of sin for tabarruj (wanton display).
It says in Fataawa al-Lajnah al-Daa’imah (17/129): There is no reason why a woman should not adorn herself by wearing makeup on her face, or kohl, or doing her hair in a manner that does not make her resemble kaafir women, but it is also essential that she cover her face in front of men who are not her mahrams. End quote.
It also says (17/128): Using kohl is allowed in Islam, but it is not permissible for a woman to show any of her adornment, whether kohl or anything else, to anyone other than her husband or mahrams, because Allaah says (interpretation of the meaning):
“…and not to reveal their adornment except to their husbands…”
And Allaah knows best.