STEP1

Clone letsencrypt git repo;

git clone https://github.com/letsencrypt/letsencrypt

cd letsencrypt

sudo ./letsencrypt-auto --help  

Ensure your webserver is not running
For my case - Nginx

sudo service nginx stop

STEP2

Run the script - Change the YOUR_DOMAIN.COM to your own domain before running. Also make sure to include the www. subdomain for one of the entries as shown;

./letsencrypt-auto certonly --standalone --standalone-supported-challenges http-01 -d www.YOUR_DOMAIN.com,YOUR_DOMAIN.com --renew-by-default

If successfull the Cert files will be stored in the following directory;

sudo ls /etc/letsencrypt/live/www.DOMAINNAME.com

Check if files have been created


FIX PERMISIONS

sudo chown root:www-data /etc/letsencrypt/live /etc/letsencrypt/archive/
sudo chmod 750 /etc/letsencrypt/live/ /etc/letsencrypt/archive/