I currently have a site (for illustrative sake, let's call it www.foobar.com). Earlier this year, I purchased a new domain (let's call that www.foobarnew.com). The reason for this new domain was for something unrelated to the foobar.com site, but in any event, it needs to be an active URL. As a result, I wanted it to redirect to www.foobar.com, returning a 301 HTTP status code in the event that a SE picked it up for some reason.

Due to a DNS gaffe, the foobarnew.com URL was mapped directly to the foobar.com, which was somehow being picked up by Google. Fearing the duplicate content ban, I had the DNS changed so that it now redirects to foobar.com with the 301 status code. However, Google has some pages indexed under the foobarnew.com domain.

If I use the "Remove Your URL" page on Google (http://services.google.com/urlconsole/controller), will it remove only foobarnew.com pages? Or will it also remove the foobar.com pages?

Google will remove only the url you entered into the URL removal tool.