$filename comes from just a few lines earlier in the documentation. Of course, a few lines later, the docs suggest this code instead:

use CGI;
my $query = CGI->new();

my $fh = $query->upload('uploaded_file');
while (<$fh>) {
    print;
}
[download]

Assuming you've created a form that posts to the script correctly, uses the POST method, uses multipart/form-data encoding, and contains a file upload field named uploaded_file, this will work for you.