Not that tricky finally, I just had to turn things around.
This is my config :
<VirtualHost *:80>
ServerName https://www.mydomain.com
DocumentRoot /var/www
</VirtualHost>
<VirtualHost *:80>
ServerName mydomain.com
ServerAlias *.mydomain.com
DocumentRoot /var/www/wordpress
<Directory />
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ – [L]
# uploaded files
RewriteRule ^files/(.+) wp-includes/ms-files.php?file=$1 [L]
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ – [L]
RewriteRule . index.php [L]
</Directory>
</VirtualHost>
I kicked out the .htaccess and everything is running well !
My website run at https://www.mydomain.com and blogs run at subdomain.mydomain.com
By the way thanks for the support ??