secondary domain also resolves as directory

Is there a way to prevent a secondary domain from also resolving as a directory under the primary domain?

Example:
http://primarydomain.com/ has directory structure:
root/public_html/secondarydomain.com/

where the secondary domain is a directory within the public_html (www) directory of the primary domain and DNS pointer is set to http://secondarydomain.com/

but it can also be accessed via:
http://primarydomain.com/secondarydomain.com/

I would like accesses to the directory to be ignored / disallowed. Is this something that can be resolved using .htaccess?

thanks,
Tom