你做什麼了?That is not the best translations of (What did you do?),maybe this one is better:你做了什么？ “了” in this sentence also means an action has been completed, but the questioner didn't know what things have been done by the person he/she asked. In most case, this sentence express a kind of anger(often we'll use "!" replace the "?")/doubt/surprise... Btw, it's incorrect, u should say:谢谢你回答我（thanks for answering me）, or 谢谢你的回答（Thanks for ur answer）。 ^ ^ Hope that will help u.

First, when 了 comes right after the verb, it may be not perfect tense, and could be present progressive tense, for example: 他睡觉了 （He is sleeping.） If you want to express something has been done, you can add 过 between the verb and the noun. for example: 他睡过觉了 （He has slept. It indicates that he is awake now） Why 了 in the end of the sentence here? My answer is that We like to add a noun after a verb to make the meaning specific. 你做什么了？ 做 is verb, 什么 is noun, we regard them as a whole. for example: 我在吃饭， 吃 is verb 饭 is noun. we don't use 吃 alone here. but in some cased noun can be omitted. 谢谢您应对我 is not correct, you can say 谢谢你的回答！

Besides the usage you know, 了 also indicate 'change in situations'. i.e. 下雪了，(because usually there is no snow, now there is, so situation-change). Then it's Past Tense: What DID you do? So it's: 你做什麼了?(YOU+DO+WHAT+PAST TENSE INDICATOR)= 你做了什么(YOU+DID+WHAT)？ Last one, 谢谢你的回复 reply / 回答 answering / 答案 answer. etc.