Sounds like you need a hash (untested):

my %seen;
my %tree;
while (<>)
{
    chomp;
    # change this to match, as you didn't give a good example
    my ($file,$line,$rule) = m/^"(.*?)"\s*(\d+):\s*[^:]*?:\s*(\d+):/;
    unless ( exists( $seen{"$file,$line,$rule"} )
    {
        push @{$seen{"$file,$line,$rule"}}, $file,$line,$rule;
        $tree{$rule}{$file}{$line} = 1;
    }
}
[download]

Update: changed %hash name to %seen to match my declaration.