use strict;
use warnings;
use Fcntl qw( SEEK_SET );

 .  .  .

my @bytes;
{
   my $input_location = 40;
   local $/=12;     # Read 12 bytes
   open my $INF, '<', 'foo' or die;
   seek($INF, $input_location, SEEK_SET);
   my $t = <$INF>;
   @bytes = split //, $t;
}

# Do something with them
@bytes = shuffle @bytes;

# Write them to another file
open my $OUF, '<+', 'bar' or die;
my $output_location=1234;
seek($OUF, $output_location, SEEK_SET);
print $OUF, join("", @bytes);