There are myriad ways. Lots of guys have been talking up the "precision ground" stones lately. Those are ground flat on a surface grinder with a diamond wheel.
They can also be flattened with a good quality electroplated diamond hone.
They can be flattened with loose silicon carbide grit on a lapping plate or a very flat piece of glass.
They can be flattened with wet/dry sandpaper with a flat backer like a lapping plate, flat piece of glass or a cheap import surface plate.
And finally, there is the very first method I ever used as a young apprentice, which is to mount a diamond nib in a flycutter and mount it in a mill, then use that to basically "mill/dress" the stone surface flat. (That one was a method I made up on the fly when frustrated with a non-flat hone and had no other method available in a pinch, but it worked).