Neto will not allow you to delete a payment method however you can make the payment method inactive and not visible to your customers.
To mark a payment method inactive:
From the Neto Dashboard, select Setup & tools > Payment Methods.
Click the Configure button on the method you want to deactivate or hide.
Click on the the credit card option (Visa/Mastercard) you wish to edit.
Set Active/Enabled and Show on Website to off and Save Changes.