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In Webmaster Tools, set the subdomain up as its own site and verify it
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Put on the robots.txt for the subdomain (beta.website.com/robots.txt
User-agent: *
Disallow: / -
You can then submit this site for removal in Google Webmaster Tools
- Click "optimization" and then "remove URLs"
- Click "create a new removal request"
- Type the URL "http://beta.website.com/" in there
- Click "continue"
- Click "submit request".