My solution (clumsy as usual):

my @array = qw( ...);
my @remindexes = qw( ... );
my %remindexes;
my @newarray;

for (@remindexes) {
    $remindexes{$_}++;
}

for (my $i = 0; $i <= $#array; $i++) {
    push @newarray, $array[$i] if !$remindexes{$i};
}
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Of course, if you would setup the indexes to remove into a hash from the beginning, you could omit the first step.