Assuming it's an Ehrlenmyer flask, you pretty much have to break it to extract the seedlings without damage. Trying to fish them out of that narrow neck without doing so is a pain.
The idea behind the fish tank is to maximize the humidity around the seedlings. So far, for their entire lives, they have been in a 100% humidity environment, so they'll need to be "hardened off" and transitioned to dealing with your ambient conditions.
Most folks will put those seedlings into one or two "community pots", depending upon their size. After potting them up and watering them in, in lieu of a tank, you can just invert a clear plastic bag over them to trap the humidity. No need to seal it. Keep them warm and shady, and moisten the potting medium as needed.
Once you see that they are stable, and maybe even growing a bit, remove the bag for an hour for a week, then two hours, then three. If the leaves look OK after a week of the three hours of exposure, I'd leave them out all day, and enclose them at night for another week,then ditch the bag.
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