Seems grepping, as hdb suggested, may produce your desired results:

use strict;
use warnings;

my @DIR = qw{functions/myfunc.hml perltest/abs.hml perltest/abs3.hml p
+erltest/abs4.hml perltest/acos2.hml perltest/zeros17.hml};
my @filtered = grep !m{^perltest/}, @DIR;
print "$_\n" for @filtered;
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Output:

functions/myfunc.hml
[download]