Maybe instead of going the "stressful" way to remove each and every old URL, simply create 301 redirections from all the en/de.example.com URLs to your example.com.
This is probably a better approach for removing URLs of old subdomains, as eventually Google will find out that all the old subdomains URLs have permanently moved to your new one, and will remove/replace them in its index.
Same time, you can keep driving traffic from old indexed URLs to your site, for as long as they will keep appearing in SERPs, instead of killing all this traffic at once by terminating the subdomains - resulting to a non resolving url.
Keep in mind that time is essential here, as the procedure of removing old URLs from Google's index is slow, whatever way you go.
You can use .htaccess for this.
To redirect from en.example.com/url to example.com/url:
RewriteEngine on
RewriteCond %{HTTP_HOST} ^en.example.com$
RewriteRule ^(.*)$ http://example.com/$1 [R=301,L]
To redirect requests for en.example.com/url to example.com:
RewriteEngine on
RewriteCond %{HTTP_HOST} ^en.example.com$
RewriteRule ^(.*)$ http://example.com/ [R=301,L]
Notes:
You will need the DNS back, so the subdomains will keep resolving.
You may also want to implement more techniques, like adding entries in your robots.txt, or implement noindex,nofollow's for the old subdomain URLs.