I have a site which was temporarily available at both example.com and www.example.com. All traffic to example.com is now redirected to www.example.com, however during the brief period that the site was available at the naked domain, Google indexed it.

So Google now has two versions of every page indexed:

www.example.com
www.example.com/about_us
www.example.com/products/something

...

and

example.com
example.com/about_us
example.com/products/something

...

For obvious reasons, this is a bad situation, so how can I best resolve it? Should I request removal of these pages from the index? There is still content at these URLs, but they now redirect to the www subdomain equivalent.

The site has many hundreds of pages, but the only way I can see to request removal is via the Remove outdated content screen in Webmaster Tools, one URL at a time.

How can I request removal of an entire domain (ie. the naked domain) without it effecting the true site located at the www subdomain? Is this the correct strategy given that all the naked domains now redirect to their www equivalent?