Since the 3DS saves data to the cartidge, there isn't an option to delete/wipe the savegames. However, you can overwrite the exisiting savegames with 0% saves.

When you start a new game, select one of the save slots containing a save you previously made, confirm you want to overwrite the save, then exit the game and repeat with the other save slot you want to overwrite. (You can verify each save is back at 0%, by selecting Load, viewing the save slots, and then cancel without actually loading either game.)