I agree, if you can do it in memory, then do it in memory. Also the Standard Perl i/o mechanisms are incredibly slow. I would recommend File::Slurp (supports slurping and spewing). I used it once in a programm that had to modify roughly 1000 files. Compared to standard slurping like:

{
local $/ = undef;
my $wholefile = <$FH>;
}
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it was 15 times faster (it now takes roughly 3 minutes, while with standard perl mechanisms like the one abough, it took 45 minutes). It might even be that both (Input and Ouput Data) fit into main memory - if they do and if such memory consumption isn't a problem, then simply do it - its much faster.