Like regular withholding...the taxes taken out when you withdrew the $$....those were just a pre-payment against the $$$ that are eventually assessed when you actually prepare your taxes.
Example: say you had 10% Federal taxes withheld....you get credit for those taxes paid at tax time, but if you are in the 12%, or 20% or higher tax bracket when you actually file, then you will owe some more to make up the difference.
Just make sure you enter the proper $$ that were withheld in box 4 of the 1099-R form when you prepare the software form.