Make up isn't magic, if a girl is super fugly makeup isn't gonna suddenly make her hot. And I'm not sure why this bothers you so much, if the girl isn't as good looking without makeup, at least she makes an effort to solve the problem.
To actually give an answer though, I think you can tell by just looking at facial structure and seeing how much makeup is visible. If its all layered on, you probably aren't interested in her.
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Go for it, you don't need us.. You'll never forgive yourself if you don't try anyway.
Rejection is easily forgotten, regret isn't.