I used to have two subdomains on my website, each one having one page only. The thing is, I decided to remove the subdomains, but to not lose the links pointing to them, I redirected them to the main domain. I thought that Google would understand the redirects and remove them from the index, leaving only the main domain, but instead it's now listing the subdomains as duplicated content. So, how do I make Google remove the subdomains from the index, without losing their links traffic and PR? Ps: my domain is http://www.onlinelogomaker.com. If you make the Google query "site:www.onlinelogomaker.com /"you can see the indexing issues.
If you remove your sub-domains you will get a "server not found" page. (thought i'd put that out there.)
I think I found the solution: http://googlewebmastercentral.blogspot.com/2009/02/specify-your-canonical.html