How about something like this (this does depend on them being sorted shortest to longest): 
my @data = sort { length($a) <=> length($b) } qw(
    2N0472|6N8595|9L1366|1189902|1413983|8B2026|1M3381|7K3377|3H5788|1
+F7854|8W1152|8R0721|9C5344|6W6672|­9G7101|3023908|6Y1352|4P0489|27578
+03
    3419308|3514531|3525716|3557019|3586192|3635776|3783741
    3T3625|6T7765|9L1366|1189902|1413983|8B2026|1M3381|7K3377|3H5788|1
+F7854
    3T3625|6T7765|9L1366|1189902|1413983|8B2026|1M3381|7K3377|3H5788|1
+F7854|8W1152|8R0721
    3T3628|6T7765|9L1366|1189902|1413983|8B2026|1M3381|7K3377|3H5788|1
+F7854|8W1152|8R0721|9C5344|6W6672|­9G7101|3023908|6Y1352|4P0489|13369
+34
    4N4906|6N6481|9L1366|1189902|1413983|8B2026|1M3381|7K3377
    4N4906|6N6481|9L1366|1189902|1413983|8B2026|1M3381|7K3377|3H5788
    6N7936|6N5049|9L1366|1189902|1413983|8B2026|1M3381|7K3377|3H5788|1
+F7854|8W1152|8R0721|9C5344|6W6672|9G7101|3023908|6Y1352|4P0489|275780
+3
    6Y0248|6T7765|9L1366|1189902|1413983|8B2026|1M3381|7K3377|3H5788|1
+F7854|8W1152|8R0721|9C5344|6W6672|­9G7101|3023908|6Y1352|4P0489|13369
+34
    6Y0248|6T7765|9L1366|1189902|1413983|8B2026|1M3381|7K3377
    6Y0248|6T7765|9L1366|1189902|1413983|8B2026|1M3381|7K3377|3H5788|1
+F7854|8W1152
);
my %uniq;

foreach my $elem (@data) {
    my @parts = split /\|/, $elem;
    foreach my $p (0 .. $#parts) {
        my $e = join '|', @parts[0..$p];
        delete $uniq{$e} if exists $uniq{$e};
    }
    $uniq{$elem} = 1;
}

print "$_\n" for keys %uniq;

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In reply to Re: Best method to eliminate substrings from array by Paladin
in thread Best method to eliminate substrings from array by catemp

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