I would change:

# output file

$newfile = ">./batch_test.txt";

# open the new .txt file

open(BATCH, "$newfile") || die "Can't open $newfile : the batch_test file. $!";

to

# output file

$newfile = "./batch_test.txt";

# open the new .txt file

open(BATCH, ">$newfile") || die "Can't open $newfile : the batch_test file. $!";

and

print $newfile;

print "\n";

to

print BATCH $_,"\n";