"Nae bother" in the context of "not a problem, not an issue" would be 大した問題じゃない taishita mondai ja nai
("It's not a big problem"). You could then tweak for particular Japanese dialects.
Tokyo Shitamachi - 大した問題じゃねえよtaishita mondai ja nei yo
Osaka/Kansai region - 大した問題やないでtaishita mondai ya nai de
"Nae bother" as a response to "thank you", would simply be いいえ iie
(possibly doubled for effect), and with friends simply, いいよ ii yo
(it's good), which can also be modified for dialects, e.g. Osaka ええで ei de
Remember, there are three important things when asking for translation: context, context, and context. Also, don't forget context.