You don't appear to be writiing anything to the output file.
May I suggest the following

#!/usr/bin/perl -w

use strict;

open INPUT, 'your_input_fiel.txt';
open OUTPUT '>your_output_file.txt';

while (my $line = <INPUT>)
{
    chomp $line;
    $line =~ s/hello/goodbye/gi'
    print <OUTPUT> $line;
}
close INPUT;
close OUTPUT;
[download]

Hope this helps