There are several ways to accomplish this task but what I have found to be easiest is to draw a hole a .250 diameter. Setup a new tool in your library that has a kerf width of .249. Create a toolpath and select all the 1/4" holes that you want a pilot hole for. Select your tool from the previous step. Make sure it’s set to in computer, no lead in, no lead out and pierce clearance set to zero.
Check the simulation to make sure the toolpath is inside if the hole.
When you run the gcode the machine will create a hole the diameter of actual kerf width plus .001"
Speaking out of my ass here as I haven’t tried it and I’m a total noob, but couldn’t you just do the above but turn the amperage down so low it doesn’t pierce through?