No, they should be ok and eventually drop out. I wouldn't try to remove them now. What I do is siphon about 3/4 of the wort with my autosiphon, and then pour the rest through a strainer into my fermenter. Some people like to whirlpool their wort before transferring to the fermenter- it leaves a big pile of stuff in the center and then you can siphon from the side. (I hope that makes sense). If the hops make it into the fermenter, though, it's really not a problem though.
Broken Leg Brewery
Giving beer a leg to stand on since 2006