If I want to get are clear surface of plastic, what is better- 2 flute drill or a cutter (rottating knife)?
Excuse me for this is a CNC problem and not Mach3.

You won't get a clear surface, no matter what tool you use.  After cutting, pass a flame over the cut edge to melt it, and it will flow into a glass-smooth, crystal clear surface.  But, too much, and it'll catch fire.

Regards,
Ray L.

All depends upon your application. I'm familiar with the engraving of the plastic and then using LED's around the perimeter to turn the placard into sign that picks up the frosted area you may have just engraved. There's videos on YouTube of such. However, if you flame polish the engraving hence making it clear, you may destroy your intent for the sign/placard.

Flame polishing works great on the edges though! Videos on YouTube for that too.