Unless if your LED is already a flat-top, you'll have to grind/sand/cut it down to that the top is flat, and not far (within 1mm or 3/16") from the LED glowing element. There's not that much room to shove a whole LED in.
We used a sanding belt to bring it down to size, but see how it leaves the top an opaque white? Here's a trick: Rub the flat face against a sheet of paper for a full minute. It brings up the polish quite well, and if the face is fairly smooth, you can almost get it back to stock clarity.