The -i command-line switch modifies each file in place. It does so by creating a temporary file (but Perl takes care of the details/bookkeeping).

You can also do this yourself of course:

open(OLD, "< $old")       or die "can't open $old: $!";
open(NEW, "> $new")       or die "can't open $new: $!";
while (<OLD>) {
    # change $_, then...
    print NEW $_          or die "can't write $new: $!";
}
close(OLD)                or die "can't close $old: $!";
close(NEW)                or die "can't close $new: $!";
rename($old, "$old.orig") or die "can't rename $old to $old.orig: $!";
rename($new, $old)        or die "can't rename $new to $old: $!";
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Source Perl Cookbook.