Mod_rewrite and subdirectory access - apache

Question

I'm trying to deny access to couple of subdirectories (when using specific url) that are in www-root.
My goal is:
Make domain.com/subdir{1-3} to deny access.
Make subdir{1-3}.domain.com to point to %{DOCUMENT_ROOT}/subdir{1-3}. Already works.
I want to write rules to httpd.conf without having to use .htaccess files and use only one Directory section if possible.
Here's what I've tried:
<Directory "/var/www/subdir1">
<IfModule rewrite_module>
RewriteEngine on
RewriteCond %{REQUEST_URI} ^/subdir1 [NC]
RewriteRule ^.* - [F]
</IfModule>
</Directory>
But no go.
//E
Got it working, here's what I did:
<Directory />
<IfModule mod_rewrite.c>
RewriteEngine on
RewriteCond %{REQUEST_URI} ^/subdir1/ [OR]
RewriteCond %{REQUEST_URI} ^/subdir2/ [OR]
RewriteCond %{REQUEST_URI} ^/subdir3/ [OR]
RewriteCond %{REQUEST_URI} ^/subdir4/
RewriteRule .* - [F]
</IfModule>
</Directory>
Is there anything I should change to make it more safe?
Everything works except subdir3 which points to ownclouds root dir. It must have something to do with ownclouds own rewrite rules:
<IfModule mod_rewrite.c>
RewriteEngine on
RewriteRule .* - [env=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
RewriteRule ^.well-known/host-meta /public.php?service=host-meta [QSA,L]
RewriteRule ^.well-known/host-meta.json /public.php?service=host-meta-json [QSA,L]
RewriteRule ^.well-known/carddav /remote.php/carddav/ [R]
RewriteRule ^.well-known/caldav /remote.php/caldav/ [R]
RewriteRule ^apps/calendar/caldav.php remote.php/caldav/ [QSA,L]
RewriteRule ^apps/contacts/carddav.php remote.php/carddav/ [QSA,L]
RewriteRule ^apps/([^/]*)/(.*\.(css|php))$ index.php?app=$1&getfile=$2 [QSA,L]
RewriteRule ^remote/(.*) remote.php [QSA,L]
</IfModule>
Tips are welcome.

Answer 1

Try:
RewriteEngine On
RewriteCond %{HTTP_HOST} ^(www\.)?domain\.com$ [NC]
RewriteRule ^subdir1 - [L,F]
RewriteCond %{HTTP_HOST} ^subdir1\.domain\.com$ [NC]
RewriteCond %{REQUEST_URI} !^/subdir1/
RewriteRule ^(.*)$ /subdir1/$1 [L]
for "subdir1".