The first part, where you create @tempArray, is better written as:

my @tempArray = grep { /^A/ } @array;
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So, your entire part can be rewritten to:

foreach my $ref (
    sort {
        substr($a, 1) <=> substr($b, 1)
    } grep {
        /^A/
    } @array
) {
    ... do whatever ...
}
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