Uncharted was one of the few PS3 game that tried to implement its own reward system with medals. Now that Sony got around to releasing the Trophy system and Uncharted is going to be one of the first games to receive a retrospective update to allow trophies to be earned through the game. The outlook is not all blue skies and puffy clouds, the trophies will not be automatically given for past playing, you will need to start a new game if you want to earn some trophies.
We weren’t able to award Trophies retroactively through this patch. This was done so that everyone receives their Trophies fairly and can’t take advantage of the game saves we’ve seen floating around. That means you will have to start a brand new game—without any medals or rewards unlocked—and play through Uncharted to get Trophies.