We want to be able to programatically create new custom domains using Netlify. This will allow us to automate and create easy interfaces to serve many small micro-sites.
- Custom Domains on docs.netlify.com 
# On the command-line
We can use the netlify CLI to create a custom domain.
netlify api createSite -d '{ "body": { "custom_domain": "my-site.my-domain.com", "name": "my-site.my-domain.com" } }'
See - answers.netlify.com
# Using the API
Alternatively we can use the Netlify API to acheive the same thing with json-rpc call:
- createSite on open-api.netlify.com
# See also - Netlify API