#!/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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Consider the following instead:

use strict;
use warnings;
use autodie;

open my $FILE1, '<', 'input.txt';
open my $FILE2, '>', 'output.txt';

while (<$FILE1>) {
    s/^HDR.{47}|FTR.+//;
    print $FILE2 $_;
}

close $FILE1;
close $FILE2;
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• autodie will trap the file i/o errors (you're not handling these, but you should)
• Use only lexical (my) file handles
• Use while to iterate through the file
• The two substitutions were combined into one

If FTR marks the footer to the end of the line, you can just use FTR.+ to remove it, since in your example there were only 30 characters left--including FTR. However, it's certainly OK to use FTR.{27}, if you prefer.

while ( <$FILE1> )
{

s/^HDR.{47}//;
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