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The only plywood I cut is 1/2" Baltic Birch and most of the time I use a 1/4" downcut spiral 2-flute bit. The edges come out clean. Are you cutting too much in one pass, possibly? I take a roughing pass and then come back with a final pass to remove the last 0.005". I do the same thing when I engrave with a V-bit, too.
This is the only photo I have of a freshly cut piece and you can see the edges are pretty clean.
David
PS - I'm using a Whiteside 1/4" spiral downcut bit but they also have it in upcut. Matter of fact, I have both upcut and downcut in 1/8", as well.