You could filter is out. Depending on how you are transferring it. You could put a strainer bag or grain/hop bag over the end of your auto-siphon to help keep the unwanted grains out. What you don't want to do is over expose it to unwanted oxygen and making your beer taste stale. So do not run it through a screened funnel or anything like that. I just let everything settle to the bottom of my fermenter and avoid jamming my auto-siphon down into it.
How were you planning on transferring it?