Dont file the ones you have down.
From memory ,inside the barrel when you remove it are 5 slotted plates which are individually numbered 1, 2 or 3 as I recall. If you use the correct plates in the barrel, when you insert the key all plates will become flush with the cylinder.
If you go to a dealer they will probably have a small pile of individual plates that you can select from to re-key your existing locks. Every key barrel they sell has a selection of these plates in the kit supplied, most of which they don't use again when they have finished working on a new lock. You can also re-use the existing plates from your locks if necesary.
The job is one of trial and error and takes about 5 minutes to do. Once you have the plate sequence for one lock barrel, repeat this sequence with the other barrel.