My grandmother does make homemade truffles and they do indeed taste delicious... and are indeed very messy.
Ice cube trays would make rectangular truffles, which would be less mess and taste the same, but they would cause questions about the shape. At least I think people would question it. Do they not even notice the shape when you make truffles?
Also what do you use in truffles? My grandmother uses dark chocolate cake and peach jam, mashed up and rolled in a ball, then dipped in chocolate.