Receiving an email from Google saying that they have noticed unnatural links associated with your website is never a good thing. The best outcome still involves losing organic search traffic from Google for at least some time, plus the email means you have work to do really quickly.
Search Engine Watch writer Chuck Price has seen webmasters respond to manual penalties and many of them actually make their problems worse, especially when they panic. Webmasters who panic when they receive a manual penalty website tend to fly into manic states running around doing the first thing they can think of to try to get the penalty fixed; thoughts like filing reconsideration requests before actually fixing the problem.
If you’ve received an email about unnatural links or manual penalties, take a minute to breath. There is no reason to panic. You have to do some work to identify the issues and fix your site’s linking problems, but panicking isn’t going to get that done any faster, and might blow your one chance to get your links reconsidered by Google in the near future.
Once you’re calm, it is time to get to work. Price has suggestions for how to get your page back in order no matter how many bad links you have. However, if you have been actively building thousands of unnatural links, you will have to make huge efforts to make up for the spamming.