One way is to open 2 filehandles thus:

use strict;

open(my $reader, '<', 'file.to.read');
open(my $writer, '>', 'file.to.write); # will be truncated

while(<$reader>)
{
  # do desired mangling here
  print $writer "$_";
}
[download]

This will copy file.to.read into file.to.write unchanged.

If you do stuff in the while where the comment is before writing then print the variable you want into the new file you have a filter.