How do you mean? CNP is used when the customer has given their card details and permission to charge the card for goods or services but is not there to sign the slip/input their PIN.
Do you mean how does a merchant ensure that the customer doesn't deny that they took part in the transaction?
Things like checking the address, the cvv number on the signature strip etc. if that's what you mean. If not, then what do you mean?
There are various codes used in credit card transactions. There is a specific code for 'Customer Not Present' so the online checking systems can identify it as a 'more risky' transaction and process it appropriately.