If your array is too big to copy it, try something like this:

for my $m (reverse 0 .. $#molecules) {
    if ($molecules[$m] eq "\n"){
        splice (@molecules, $m, 1);
    }
}
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That's very inefficient, O(N^2) worst case under the hood. If your data is so big it doesn't fits in memory, it is not a good solution either. Note also, that the grep solution is swap-friendly as it access memory in a sequential manner.

Anyway, if you want to minimize memory usage and still be O(N):

my $to = 0;
for (@m) {
  $m[$to++] = $_ if $_ ne "\n";
}
splice @m, $to;
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Unfortunally, if the array is large, and there's a significant number of elements "\n" in the array, the repeated splicing can be slow. splice() is an O(n) operation (with n the length of the array), and that's a tight worst case bound (splice may require shifting half the array). If you have a large array, and cannot afford to copy, you can still remove the offending elements in situ:

my $j = 0;
for (my $i = 0; $i < @molecules; $i ++) {
    $molecules[$j++] = $molecules[$i] unless $molecules[$i] eq "\n";
}
splice @molecules, $j;
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for (my $i = 0; $i < @molecules; $i ++) {

Should n't that be as



for (my $i = 0; $i < scalar(@molecules); $i ++) {
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