It might be easier (and faster asymptotically) to just build a new array in this case:
my @new;
foreach my $array ($values) {
my @inner;
foreach my $value ($array) {
push @inner, $value if $value ne "UNKNOWN"
}
push @new, \@inner
}
$values = \@new;
Or, if you like to be fancy:
$values = [ grep { $_ = [ grep { $_ ne "UNKNOWN" } @$_ ] } @$values ]
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