Certainly, you can read a file into an array, and process that; whether it's a good idea depends on the size of the file. For reasonably sized files (a few megabytes), it's likely to be the choice which uses the least wall-clock time. If the file is very large, something like Tie::File may be appropriate.

At least until you get the code debugged, I would make sure that you create a backup file when you do an "edit in place."