You may have received a manual Google Webmaster Tools notice informing you that Google has detected unnatural links to your site. You will now need to remove those links, clean up your site, and make a reconsideration request. Upon successful acceptation of your request, the penalty will be removed and your website will be again indexed by Google bots.
However, Google does not specify how to specifically apply for a reconsideration request and the content to be included in that request. You can begin by identifying and remove unnatural links and disavow links that cannot be removed after repeated efforts.
You should also eradicate or nofollow links in case your penalty is related to onsite issues including selling of links that can pass PageRank. Once you have taken all necessary steps to remove those bad links that got your site into trouble then you also need to inform Google about the steps you have taken.
Rather than merely filing a reconsideration request, a better option is to provide proof of your efforts to Google. You can begin by using only Google documents to communicate with Google since Google employees prefer opening such docs and avoid opening others to prevent viruses from infecting their systems.
Your Google links spreadsheet should involve details such as records of emails received and sent along with screenshots, if possible to show Google that you have made all necessary efforts to resolve the issue from your end.
In case a SEO company hired by you has made link purchases or engaged in inserting spam links on your orders then you will need to mention these facts while making a reconsideration request. If you have fired the SEO company for actions not in line with Google Webmaster guidelines, you can mention this information to show Google that you have committed an unintentional error and that heads have rolled.
You should also mention from where you have purchased the offending links and can also mention the SEO firm hired by your company. You also need to mention information about your disavow.txt file in your request.
In case you have received a manual penalty then your reconsideration request will also be processed manually by a Google employee. In case you have received an automated warning then you will again receive an automated message informing you that no spam action was recorded on your repaired site.
You must remember not to use aggressive language in your reconsideration request. Reminding Google that you spend a fortune on AdWords every month or badmouthing Google and its employees in your reconsideration request will not speed up the process, but could most certainly delay it.
It could take anywhere between 2 to 6 weeks for your reconsideration request to be processed and a response evoked from the Google team handling your request.
If you have received a manual penalty from Google stating that you have violated Google Webmaster Guidelines then you will not only need to clean up your website, but will also need to file a reconsideration request to get back into indexing by Google.
A detailed and courteous request using Google documents holds the most promise of positive action from Google within the shortest possible time.