So this is the one that i tried and it works. Thanks kenosis and others for taking the time. 
#!/usr/bin/perl
use strict;
use warnings;

open FILE1,"input.txt";
open FILE2,">>output.txt";
foreach my $line ( <FILE1> )
{
$_= $line;
s/^HDR.{47}//;
s/\KFTR.{27}//;

print FILE2 $_;

}
close FILE1;
close FILE2;

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this made the most clarity for me. I am assuming that the entire file doesnt gets stored in the $_ in this approach, correct me if i am wrong. and the file is only getting read one line at a time. This i want to make sure so that it performs well when i actually test with the huge file.

In reply to Re^4: header footer by gupr1980
in thread header footer by gupr1980

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