In the sixth level (Small pink flower) you need to completely awaken all areas. You can tell if an area has not been awakened if it is gray. For the most part areas are awakened by blooming flowers or destroying antennas, however there are a few places that are awakened just by flying near them. There are some areas in the final stretch that may stay gray no matter what you do, though you should still get the Trophy.
Credit to PLYMCO_PILGRIM from the PS forums.