A Duelist's Main Deck is the pile of at 40 to 60 cards, placed on the Deck Zone. The Main Deck is, essentially, all the cards the duelist will be playing with in Duel. This Deck contains all the Trap, Spell and Monster Cards the duelist will be using, with the exception of Fusion Monsters and Synchro Monsters, which are placed on the opposite end of the main Deck Zone in the Extra Deck. Whenever a card effect is activated that lets you search your Deck and select a card(s) to place in your hand, on the field or in the Graveyard, you should always shuffle your Deck to maintain fair play.
Most Decks contain approximately 40 cards, since 40 is the minimum amount of cards a Deck must have in order to be legal (not including cards in the Extra Deck). Most experienced Duelists will argue that you should stick to the minimum because it increases the chances of you drawing your best card(s).