The best thing to do is to just rack the beer out from under them, into a new (secondary) vessel.
How did you fill the fermentor? Ideally you should adjust your technique a bit so that the hop trub (including seeds, etc) don't make it into the fermenter. Brewers will often use a false bottom (as I do), or whirlpool to seperate the trub from the wort.
Side question, are these homegrown hops? In general, commercially packaged hops should have very low (if any) seed content. The only time I have ever found a large number of seeds in my brew kettle is when I was brewing with homgrown hops I didn't quite harvest in time. (they still made fantastic beer though)