If your file is not huge, you can store the lines in an array instead of a temp file (UNTESTED):

#!/usr/bin/perl
use strict;
use warnings;

my $file = "c:\\tmp.txt";
open( my $fh, "<", $file ) or die $!;

my @array;
foreach (<$fh>) {
    chomp;
    if ( $_ =~ m/^\s+\d/ ) {
        $_ =~ s/^\s+//g;
        $_ =~ s/\s+$//g;
        $_ =~ s/\s+/,/g;
        push @array, "$_  \n";
    }
}

my $OUTNET2 = "c:\\final.txt";
open my $out, '>', $OUTNET2 or die $!;
my %hash;
for (@array) {
    my $key = join ',', ( split /,/ )[ 1, 2, 3, 4 ];
    print $out $_ unless $hash{$key}++;
}
close $out;
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Note that I used your @array, which you didn't seem to be using.