It depends on the job but in most cases it would not matter. If you mill last of all then the drilling marks from swarf will not show, if the finish is important drill first then machine flat surface.
If the material is difficult to machine (say 316 stainless ) then drill last as the holes can be hard on the inserts and your cost go up. If there is risk of movement in sizes you may have to rough out first and then final machine toleranced. sizes.
If you have to machine a long and difficult to hold work-piece you may be able to drill the holes first and countersink them for socket head bolts and then open the holes out last of all after machining the surface of the plate.