The easiest way is to do a find and replace. I know how to do it in MS Word (as that's what I've been using up until now) -- if you go to the advance options and make sure "use wildcards" is checked, you can simply put in [a-z] for find and whichever letter you want to replace it (I use q). Do the same for [A-Z] (which will replace all capital letters) and a couple of clicks later you'll have a letter scrambled document.

I'm pretty sure most other programs would have a similar function, it's just a matter of finding it (wildcard replacement is probably a good search term to start with).