How did your spouse contribute to her HSA? You have an overall family limit of $6900. Your need to withdraw $3450 could be satisfied by either one of you withdrawing any combination of money equaling that amount. If your wife contributed after-tax money directly, it would be much easier to have her take out $3450, so you don’t have to mess around with payroll.
Removing excess contributions is not a regular withdrawal. It requires that you notify the bank in advance, and may require a special form. The HSA bank will determine the amount of earnings attributable to the excess contribution and refund it for you.
