direct access denied on subdomain's subdirectory - .htaccess

Question

my directory:
domain.com/
-----------subdomain/
---------------------subdirectory/
I've created subdomain as subdomain.domain.com
I need to access subdomain.domain.com/subdirectory but is shows: 404
I can access domain.com/subdomain/subdirectory/
please tell me how to do that.
### EDITED ###########
My .htaccess
RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [QSA]
RewriteRule ^([0-9]+^)$ download/content/$1 [L]
<IfModule mod_php5.c>
php_value upload_max_filesize 200M
php_value post_max_size 200M
</IfModule>
if I add the following before my rule, it stops my existing. and if I add it after my rule. it doesn't execute because of [L] flag
RewriteCond %{HTTP_HOST} ^wap\.
RewriteRule !^wap/ wap%{REQUEST_URI} [L]

Answer 1

Have this rule in your root htaccess:
RewriteEngine on
RewriteBase /
RewriteCond %{HTTP_HOST} ^wap\.
RewriteRule !^wap/ wap%{REQUEST_URI} [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [L]
RewriteRule ^([0-9]+)$ download/content/$1 [L]
<IfModule mod_php5.c>
php_value upload_max_filesize 200M
php_value post_max_size 200M
</IfModule>