The biggest piece of the puzzle you need is the seek function (perldoc -f seek on your system or perlfunc:seek for a quick ref). While you can open files for both read and write access, I like to work with a scratch file. So here are the steps the way I'd do it:

open OLDFILE, $oldfilename 
 or die "Can't open $oldfilename: $!\n";
# get length of first line
my $start_pos = length(<OLDFILE>);

# now read in next 11 lines
for (1..11) {
 $_ = <OLDFILE>;
}
# we've got the 12th line in $_
# nab the 6 chars starting at the 50th position of $_
my $field = substr($_, 49,6);
#rewind to the beginning of the second line
seek(OLDFILE, $start_pos,0);

open NEWFILE, "> $oldfilename.new" 
 or die "Can't open $oldfilename.new for write: $!\n";
print NEWFILE "STring with $field in it\n";
# now write eatch line of OLDFILE INTO NEWFILE
print NEWFILE while (<OLDFILE>);
close OLDFILE;
close NEWFILE;
rename ($oldfilename, "$oldfilename.bak") 
 or die "Can't move $oldfilename: $!\n";
rename ("$oldfilname.new", $oldfilenme)
 or die "Can't create new $oldfilename: $!\n";
[download]

Yeuch that's kinda clunky, but those are the steps.

HTH