I'd strongly suggest using the machine itself to cut the holes, so the easiest way would be to draw a grid of circles with a CAD package, and then use your CAM package to pocket cut each one (with the 1/4" bit).
Even better would be to use a 3/8" bit, and place a point at the center of each hole, again using your CAD package, then create a drilling process in your CAM tool.
I use a free CAD package called ProgeCAD, and a cheap (but very good) CAM package called SheetCAM. Either of the above is easy with these two (and probably many other packages, to be honest).
I wouldn't recommend using a drill bit - especially if you are thinking of using it in your spindle. Drill bits aren't designed for use at spindle RPM speeds.