Removing sub-domain but keeping the domain

[Elight]

Hey all, I'm new here.

I've got a question concerning sub-domain, domain and google index.

You see, I've created a website on a free host, and it gave me a suddomain (mysite.subdomain.com) and I added this sub-domain to google index via add url, and webmaster tool.

But a week later I created a free domain (mysite.co.cc) and also added it to google index. Then I've read that it's not good to add both because google will think you are duplicating and will damage your rank.

So I need your help, how can I remove only my Sub-domain from google index while keeping the domain...I know about the option in webmaster tool, but I'm afraid it will erase my domain too...

All help appreciated!