Use a siphon with a cap on the tip, the end that goes into the beer.
If the seeds are small enough that you think they'll slip through the cap, you can put a hop sock, cheesecloth, or other filter on the end of the siphon in the beer. Make sure to sanitize anything you use.
But if the seeds aren't suspended in the beer, are either floating on top or settled at the bottom, then I wouldn't worry about it. If you're careful they won't get into the siphon.
What kind of seeds are they? Hops? Fruit?