A Merchant interfaces with a card holder and submits a Card Present Transaction request whilst the card holder is waiting and the card holder authenticates the transaction (typically via signature or PIN entry). In the event of a dispute of the transaction, the merchant must prove that the card holder authorized it, else merchant is liable to refund the card holder.
A Merchant submits a Card Not Present Transaction according to previously arranged agreement with a card holder. The card holder is not present to authenticate the transaction. In the event of a dispute on the transaction, the merchant must prove the card holder authorized it, else the merchant is liable for refunding the card holder.
Fully 3DSecure transactions are Card Not Present transactions with the protection of a Card Present transaction.