If you have been affected by Penguin it means you have a problem with links pointing to your site.
You need to go through the backlinks in Google Webmaster tools and check each one to see if it's a high quality link or just garbage.
Make a list of all bad links you have and submit them to Google using the Disavow tool.
That's the cleaning up process.
After that you need to start getting high quality links to your site from respectable websites / blogs / forums.
That's the only way to recover from Penguin