$total is the number of elements in @lines, not the last array index. You're looping until $i <= $total, so the last element that you're trying to access is beyond the bounds of the array. So it's undefined.

Say that your array has 5 elements:

my @lines = qw/a b c d e/;
my $total = @lines;
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$total is now 5, but the last array index is 4, because the indices start at 0. In your for loop, $i goes from 0 to 5, and when $i is 5, you're trying to access

$lines[5]
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which doesn't exist.

The solution, of course, is to change your for loop:

for my $i (0..$total-1) {
...
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Of course, if this is all you're doing, you may as well just use grep:

my $total = grep $_ ne "\n", @lines;
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