Might want to look into "larval snaggers" -- in Wilkerson's book and online.
Or you can simply scoop them out with a white cup (easier to see them if you use a while scoop).
http://clownfish.webreefs.com/breeding/
I don't like the clear bowl cause the fry attempt to swim to the light through the glass bowl - doesn't work well. They aren't all on the surface, and some will never surface.