“So have you done your taxes yet?”

The deadline for filing your tax return is April 15. Today is April 11, but you have been procrastinating and haven't sent yours in yet. So you've been thinking about taxes all weekend. You run into your neighbor and make small talk with her. This is one of the questions you ask her.

So have you done your taxes yet?

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So

This word is a common way to start a question when the question is on a new topic. In the example above, the people were probably talking about some other topic, like the weather, before the speaker asked this question.

has (someone) (done something)

In the example above, the speaker uses "have you" because doing taxes is something that everyone must do each year. So he expects the listener to do taxes. You use "have you ___?" when you expect someone to do something, and you want to check whether it's been done yet.

do (one's) taxes

In the U.S., money is usually taken out of your paycheck to pay for taxes. But once a year, you have to calculate the exact amount of tax you owe, and fill out paperwork to send to the IRS, which is a government agency that's in charge of taxes. Calculating your tax and filling out the paperwork is called "doing your taxes".