I'm not a mod_rewrite expert, I often struggle with it, but I have done this on one of my sites, it might need other flags etc depending on your circumstances. I'm using this:
RewriteEngine on
RewriteCond %{HTTP_HOST} ^subdomain\.example\.com$
RewriteCond %{REQUEST_URI} !^/subdomains/subdomain
RewriteRule ^(.*)$ /subdomains/subdomain/$1 [L]
Any other rewrite rules for the rest of the site must go afterwards to prevent them from interfering with your subdomain rewrites.