Looks to me like you're keying the hash on the wrong data -- I think you'd have an easier time if you keyed your hash on $host and stored an array of $router's for each host.

So your hash assignment would like this:

    push @{$hash{$host}}, $router;
[download]

And your current foreach loop would then be:

foreach $key (keys %hash) {
    print "$program $key $matrix ";
    print "$path/CISCO_$_.clean " for @{$hash{$key}};
    print "\n";
}
[download]