You're much better off using File::Find than reinventing the wheel like this.
Firstly, your code will only work on Windows, or any other OS where the directory separator is \. File::Find deals with this transparently. Also you're not checking for failure. What happens if the chdir ($d) fails, maybe because the directory specified in $d doesn't exist?
The first two lines to match for the current or parent directory could be rewritten as next if $file =~ /^\.{1,2}$/;.
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