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To shuffle (Japanese: シャッフル Shaffuru) is to have sufficiently randomized a pile of cards, usually the Main Deck.
Each player must thoroughly randomize (shuffle) their Main Deck where the opponent can see. The opponent must shuffle the Deck further and then cut their deck, then return it to the original owner. No additional randomization may be done to the Deck after this point.
All card searchers involve shuffling the Deck. However, some card effects involve shuffling the Deck specifically, like "Card Shuffle". In rare cases, some card may involve shuffling the cards outside the Main Deck, like "Magical Hats".
In the manga and original Japanese anime, when Dark Yugi and Pandora dueled, Pandora used the "shotgun shuffle" method at the preparation for the duel, which Yugi noted as a highly discouraged style as it will bend and damage the player's cards. This stands the same in the real world.