In the month of June, Google asked webmasters who had received a manual action notification to use "links to your site" report within Webmaster Tools for analyzing the bad links that are pointing to the website.
A Google engineer Aaseesh Marina also told that using "links to your site" section would be enough to find out the bad links to the website and submit a reconsideration request.
It was just last week that a webmaster received an unnatural link notification and one example link provided in the notification was not present in the link report in the Google Webmaster Tools.
When a question was being raised by Barry Schwartz of Search Engine Land on the same, Matt Cutts, head of search spam said:
"It’s certainly the case that we endeavor to show examples from the set of links returned by Webmaster Tools, and likewise we prefer to assess reconsideration requests on that basis of those links. However, if there’s a really good example link that illustrates a problem, we do leave enough room to share that link, especially because it can help point the webmaster in a better direction to diagnose and fix issues".
So, we can assume that even if the link example is not removed and all the bad links within webmaster tools are removed, Google might lift the manual penalty.
Google doesn't want you to remove all the bad links but want you to make significant effort, at least to remove maximum bad links.Google Prefers to Assess the Reconsideration Request on Links Provided within Webmaster Tools!,