I don't recall Thora Birch doing a nude scene in American Beauty. Mena Suvari did a topless scene and the nude shot used in the promotion with the strategically placed rose petals, however Suvari was over 18 at the time and playing a 16-year-old.
Birch was standing in front of a window and the nerdy boy next door was watching her as she took her bra off.