This is fairly easy to do using Perl's flip-flop operator:

#!/usr/bin/perl
# Open File - Read File Contents Then Modify & save contents
use warnings;
use strict;

# Specify name of file
my $data_file = 'sample.pm';

# Name of temp file 1
my $prefile1 = '/tmp/123456.beg';

# Name of temp file 2
my $prefile2 = '/tmp/123456.end';

# Open File and read it all in to rawdata
open OUTFILE1, '>', $prefile1 or die "Could not open $prefile1. <br> $
+!";
open OUTFILE2, '>', $prefile2 or die "Could not open $prefile2. <br> $
+!";
open SAMPLE, '<', $data_file or die "Could not open $data_file. <br> $
+!";

my @rawdata;
while ( <SAMPLE> ) {
    if ( 1 .. /# __START_CONFIG__/i ) {
        print OUTFILE1;
        next;
        }
    if ( /# __END_CONFIG__/i .. eof ) {
        print OUTFILE2;
        next;
        }
    push @rawdata, $_;
    }

close SAMPLE;
close OUTFILE1;
close OUTFILE2;
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By the way, you can't exclusively lock a file opened readonly. And you should import the flock constants from the Fcntl module instead of using numerical literals.