If someone says 'thank you', you can reply in a couple of different ways. We have informal and of course, formal. In a formal situation, you would simply reply, "You're welcome". Informally you would say, "No problem". You could also say, informally, "any time". It depends on the situation.
To reply with "not at all" would be a good response if someone told you, "thanks for going through the trouble of helping me". Then in my opinion you would reply, "it was NO PROBLEM AT ALL".
I hope I added some clarity to your question.