The last time I re-worked my files I took care of a few each day until the task was done. If I'm remembering correctly, I had a goal of 10-15 per day and simply set the task up as a recurring, untimed note on my calendar until all of the files were done.
The other option would be to identify a day when you don't have any scheduled appointments and try to work through as many as you can all at once. I find, though, that I get bored/sloppy pretty quickly for tasks that are necessary but utterly boring (which is how I'd characterize clearing out files!) if I try to do too much in one sitting.
Good luck!
--Marc