The classical method would be to buy an open hole flute in the first place and then put stoppers in the hole. When you want an open hole flute you pull the stoppers out.
The official line is that other wise it can't be done.
If you were planning on doing it your self then you would need an electric drill with HSS bits. If I need to explain what to do then I cannot reccomed strongly enough that you dont, but just in case, you will need high speed on the drill and low pressure and patience. You will also need a deburrer or a round file to take the swarf off the edge of the hole. I suggest that what ever you use to flean the flute out, that you get a new one to remove the swarf so you won't contaminate your normal one. I suspect that you will probably damage the pads so you will need to fit new ones. Maybe the official line is right after all.