The ways I know (absent ATP's transfer punch suggestion):
Put a stop on your milling table, but the bar up against it, and drill with a spotting drill or other variety of short, rigid drills made for milling machines. Accuracy will depend on the finish of the end of the bar, the fence, the repeatability of your vice, the rigidity of your machine and the tendency of the bit to walk. This'll probably be repeatable to within a few thousandths.
Find the end of the bar with an edge finder, do the math, go in just the right amount and drill. Accuracy will be everything in #1 except for the finish of the fence, and repeatability of the vice, but will now include the accuracy of the edge finder on whatever surface you have on the end of your bar. Unless you have a really crappy end stop and vice this'll probably have a couple of thou more error than method #1.
Since you didn't define "exact", just eyeball it and use a hand drill. Depending on the accuracy of your eyeball you can expect to be within 100 to 50 thou, this is more than "exact" enough for a great number of jobs -- but that's probably not what you meant by "exact".
3a. Clamp the bars together and proceed with 3. The match should be as close as your ability to drill a straight hole at right angles to the material.
Disclaimer: I'm a beginner and a hobbyist. Someone who's actually done this for pay will have an answer that's both faster and more accurate than the ones I gave above.
Umm, your post is a bit fuzzy about the type of holes you want to drill.
I can see you have 48 inch long pieces of rectangular aluminum stock, each piece being 1.0 inch by 0.5 inch in cross section.
You want to drill holes in the stock. I am guessing they are to go on the larger, one inch face, and travel all the way though.
And that you want the hole in the second part to be drilled at the same point along the 48 inch length.
And you want them to be placed 100%.
I don't know what 100% is, as a machining tolerance.
You need to decide, based on the functional requirements (what are these parts supposed to do?) on a dimensional tolerance for the hole locations.
Something like, first hole to be located +/- 0.005 inch at 10.000 inches along the length of the first part, and at 0.500 across the width. Second hole in second part to be located within +/- 0.001 of first hole in first part.
That sort of thing. If you give more information then folks can help you in deciding on an appropriate tolerance, and then picking the best (simplest) technique for achieving it.
An easy way to do that is to make a stop setup on your mill table such that you can locate the two bars, one at a time, by banking off the stops. Once you've drilled your first hole, replace the part with the second part and repeat. Start your hole with a center drill or spotting drill to guarantee location. If you don't have one, you can use a short split point drill, which will usually start where you aim it. If the hole size is critical, don't drill to size in one pass. Drill your hole undersized 1/64", then open the hole with the proper sized drill bit. That way you get a much cleaner hole and it's more likely to be size.
The alternative is to stack your parts and drill both of them at the same time, making sure, in both instances, that you don't drill into the table. If you can't drill off the side, make sure you are over a T slot, or place your part(s) on parallels to elevate them enough to miss the table when the drill breaks through. Use some kerosene, or WD40, to lubricate the drill. An acid or small paint brush can be used to apply it. You'll get a much cleaner hole that way, and prevent chips welding to the drill.
Others have made good ideas on which way to go for drilling. I'll add in that if you clamp the two pieces in the vise, use some 600 or finer grit sandpaper on the moving face of the vise to insure that both pieces are clamped solidly. The problem with clamping two or more pieces of stock in a vise is that they may not be exactly the same size and the moving jaw of the vise may not be exactly square to the other jaw when pressure is applied. The fine sandpaper takes up the slack in the difference between the two pieces and allows for them to be held firmlly.
-- Why isn't there an Ozone Hole at the NORTH Pole?
You've gotten some good advice from others. One thing which I have not seen addressed is whether the hole is needed within a distance from the end which is within the capability of your mill, since you say you have a small one.
If it is not (for example, a hole near the center of the length of the bars would be well beyond a range where the mill itself could be used to control the location.
So -- if you don't need the *full* length of the bars, you could drill through both bars at once so the two holes are the same position relative to the edges (and there are ways to use the mill to make sure that you are equidistant from both edges, if that matters to you). Once the hole exists, place a piece of bar stock of the proper diameter (that which matches the hole you have drilled), through both pieces, to hold them in alignment, and while they are held in alignment by the rod, move to each end, and use the mill to trim the ends to the same length. Then turn it around and do the other end. (Note, this still does not guarantee that the hole will be equidistant from both ends.)
So -- if that matters, too, then we will need to come up with something different to accomplish your requirements for accuracy, once it is redefined to allowed actual errors, instead of "100%", which is not achievable -- or if it is, you can't prove it. :-)
This risks catching a brush bristle in the works. I like to drip cutting fluid on the work with a large hypodermic fitted with a blunted needle. I'm talking a 30 to 60 cc hypo obtained from a rural pharmacy or vet supplier.