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Your technique sounds like a great way to get carpal tunnel :-) There are sooooo many holes.
There are many types of deburring tools and each has their uses. For most applications I use a piece of a vixen file, glued or screwed to a small block of wood. Mine is about 3/4 inch wide and three inches long. You need to gently grind the edges of the file smooth. Here is a link to a pix http://www.ch601.org/tools/vixen%20file.jpg
I did that when I built my first airplane, then I found the little "crank deburring tool" made deburring the next 8000 holes (set of floats) a lot more pleasant and efficient (aircraft spruce Part # 12-00622 ) Just do not counter sink, happy building!
Ditto the Scotchbrite wheel! Great for deburring panel edges and apply a slight radius to edges. One wheel will last forever.
For deburring holes, I bought an inexpensive B&D rechargeable cordless screwdriver and chucked a fluted deburring bit into it. Just push the button and spin the bit and move on to the next hole! Built the whole plane with that "cheapo" screwdriver and it still works great years later!
I did the exact same thing with the same tool as John Austin did. The B&D tool only costs $20 bucks and makes things go so much faster. If you epoxy the deburring bit to hex stock you can change bits in and out of the driver. It's also the perfect tool for small cowl and console screws, not high speed and very small. Harbor Freight makes a look alike tool for under $10.
One cautionary note........... If you are planning on polishing your skin (or if you have not decided yet and want to keep open the option of polish) do not use the "drag a file along the line of holes" deburring technique. That technique deburrs very nicely but does put fine scratches on the surface of the skin. If you are painting, the primer and finish paint will more than fill in the microscratches. If you are working on polishing the skin, you will have a lot more work to do if you need to polish out all those file marks along every single line of rivets.
I agree with Tim Juhl's first comment in this thread, using a hand held drill bit works fine for a few holes now and then but is almost a sure thing to give you hand/tendon/muscle problems if done thousands of times, get some kind of manual or power driven deburring tool.
I also agree with the warning about countersinking holes. If using the rotary type deburring tool, either power or hand turned, be careful not to cut too big a taper into the hole, those things can actually be used to countersink a hole for a flush rivet, they cut so nicely. You just want to get rid of the burrs, not the rest of the metal around the hole.
I started out with one of the "regular" deburring tools http://www.aircraftspruce.com/catalog/topages/deburringtool.php but hated it and used a 1/2" drill bit and did the first couple of thousand holes with it until I found the crank /dogleg deburring tool Harmen is talking about and threw away the drill bit (except for very tight spots). I will say one thing for the drill bit, it dramatically cranked up the number of steps I was registering on my fitbit! :-)
At the last Oshkosh, I stopped by one of those tents in the back 40 and found a great little (used) EZ Burr deburring tool for those instances where you can't get access to the back of the holes. I paid $5 each for each of the three sizes I wanted but when I got home I discovered them in aircraft spruce's catalog for like $80 each!!!! http://www.aircraftspruce.com/catalog/topages/ezburrseries.php. The replacement blades are close to $20 each for them so they are very expensive but for the $5 that I paid, I'd buy 10 the next time I see them available.
I love them to death but they really only work when mounted in a variable speed drill and you have to be very careful with them as they can cause as much of a problem as you are getting rid of if you aren't diligent with them. I don't use them for all the holes, but they are great in those instances. (You still need to debur between mating surfaces with a hook scraper or some such)