Yes, there are a couple options: webroot, in which you point it to your server's web root directory, and the full manual, which requires you to manually do everything.

https://letsencrypt.org/howitworks/

https://letsencrypt.readthedocs.org/...g.html#plugins

If you don't want to let the Apache or nginx plugins do anything with your server config, or if you don't want to stop your web server to let LE's Standalone method work, then I'd suggest going with webroot. It will put the keys and certs on your server in /etc/letsencrypt/live, and you can point your web server to them.