If the only thing you're doing inside the loop is one or two regex substitutions, and the way you describe it, the scripts sound like they're throwaways, you may want to look at the -e, -p and maybe also -i switches in perlrun, i.e. write one-liners:

$ cat foo.txt 
one
two
three
$ perl -wMstrict -pe 's/^t(?!h)/th/; s/(.)\1/$1/g' foo.txt > bar.txt
$ cat bar.txt
one
thwo
thre
$ perl -wMstrict -pe 's/th/ph/g' -i.bak bar.txt
$ cat bar.txt
one
phwo
phre
$ cat bar.txt.bak 
one
thwo
thre
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