I was told to withdraw the excess money in my HSA to avoid getting taxed. I've already used some of that since filing. Do I still need to withdraw the remaining?

[DanO]

Yes, you need to either remove the over contribution plus any earnings to avoid the 6% penalty on the calculated excess contribution, or you can leave it and apply it to this year's contribution, but this will incur the 6% penalty.

Any amount that was used for payments for medical reasons has no impact on the amount of over contribution, so the best way to handle this is to contact your HSA trustee and inform them that you would like to have the excess removed, and they will handle the transaction and send you another 1099-SA.

Click here for some good information on HSA excess contribution