If you want to replace 'thanks', you would say 'it's nothing' e.g., "Thanks for all your hard work" "It's nothing (at all)"
'Not at all' is a little different and depends on the context. For example: "I'm sorry, did you have to wait a long time for me?" "No, not at all". There are many more possibilities, examples and contexts but it's tricky and you cannot really substitute 'thanks' for 'not at all' in all situations.