How many holes do you need? Focussed ion beam (FIB) machining will give you very precise control over a small number of holes, but won't be any use to you if you need a large array of them!
I have a useful suggestion. Using the polymer pattern coated on the Al foil, you can make micro sized hole. I mean, after coating, the micro holes will be crated by hot deep process in the NaOH