When we filed for an extension in April we prepaid almost $6000 because we weren't sure how much we would owe. We didn't end up owing so how do I get that money back?

[DoninGA]

When you filed your 2023 tax return you should have entered the amount you paid with the extension.  If your total tax payments were greater than your total tax liabilities on your 2023 tax return you would have received a tax refund for the difference on the return.

Look at your form 1040 that was filed for 2023.  

The federal extension payment will be shown on Schedule 3 Line 10. The amount from Schedule 3 Part II Line 15 flows to Form 1040 Line 31

The tax refund, if any, will be shown on Line 35a

[Opus 17]

If the return included the estimated payment, and showed that you more or less broken even, then you did owe the extra money, as it was counted with your other payments and credited to your account.

If the return did not include the estimated payment, then the IRS should show a large balance on your account.  Sometimes they will automatically refund it, or they may apply it to next year.  Check your tax return to see if the estimated payment was included.  You can also check your IRS account balance here.

https://www.irs.gov/individuals/get-transcript