To empty the eggs; tap the top of each egg with the tip of a sharp knife to pierce the shell. Peel away enough of the shell to create a 1-inch hole. Empty out contents of eggs into a bowl; discard or reserve for another use. Alternatively, use an egg topper to remove top third of eggs.
Fill a large saucepan with water and bring to a boil. Place a cooling rack over a baking sheet; set aside. Add empty shells to saucepan, and boil for 10 minutes. Remove shells, and place in a large bowl of cold water. Using your fingers, gently peel away any remaining membrane from the inside of the shells. Place open-end down on cooling rack. Let stand until dry.
Place the eggs into an empty egg carton, open-end up. Using a disposable piping bag snipped at the tip, pipe about 2 tablespoons of ganache into the bottom of each egg shell to come halfway up the inside of the shells.
Knead the marzipan with your hands until pliable. Knead in equal amounts of yellow and orange food colorings, until the marzipan resembles the color of an egg yolk. Roll marzipan into twelve 1/2-inch balls; set aside.
Place the fondant in a medium heatproof bowl, and set over a pan of simmering water. Stir until the fondant is pourable, about 3 minutes. Using a spoon, add enough fondant to each egg shell to come 1/4-inch from the top. Top with the marzipan egg yolk. Will keep in an airtight container, at room temperature, for up to 1 week.