Hello and welcome to the monastery!

You have written your question, but to help you help yourself, we'll need some more answers:

What makes the third line special? Should every third line of every file be removed, or is there some criteria other than position in a file?

What code have you already written?

The third row has an "illegal" set of characters for YAML... i.e. 3: <bracket><some number><bracket> <some text> It causes issues when I run the following sample:

use File::Slurp;
use YAML::XS;
use Data::Dumper;

print Dumper Load scalar read_file('output.txt');
[download]

Sorry, the rest of the code was cut off....

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my @config;
open FILE, "<output.txt" or die $!;
while (<FILE>) {
    chomp;
    push @config, { split /[^N\n*]/ };
    # push @config, $_;
}
print Dumper( @config );
[download]

I am sure it has to do with the regexp... But I also think that I am not dealing with the file_read properly for the split to occur... TIA

"The third row has an "illegal" set of characters for YAWL... i.e. 3: <bracket><some number><bracket> <some text>"

Umm, yeah. We kind of needed to know that in the first place, since the data in your OP gives no hint that an illegal character creates the problem... and because it's just remotely possible that some of us who might offer (substantive) help might not be familiar with "YAWL."