I don't understand why you don't want C:\\c and c:\\car in your result list. From your explanation, I think your nested hash approach is an elegant solution. I have another solution that relies on the fact that a subdirectory will always sort at a later place than its parent:

use strict;
my @paths = (
          'C:\\foo\\bar\\baz',
          'C:\\foo\\bar',
          'C:\\car',
          'C:\\c'
        );

my $last = "";
my @nested;
for (sort @paths) {
    if (not @nested) {
        push @nested, $_;
    } elsif (/^\Q$nested[-1]\E\\/i) {
        $nested[-1] = $_;
    } else {
        push @nested, $_;
    };
};
print "$_\n" for @nested;
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On Windows, we have a case-insensitive file system, so we want to compare case-insensitive. This will possibly fail if you have umlauts in your directory names that should collate to the same character.