Instructions
Turn on your PS3 and a controller and navigate to the "Game" menu. The game disc for the game in question does not have to be inserted into the disc tray.
Select "Game Data Utility" from the Game menu and select the desired game file from the list of games.
Press the "Triangle" button on your controller and select the "Delete" option.
Select "Yes" and then press the "X" button on your controller to finish the game file deletion.