After cleaning and securing your site, you must “Request a Review” through Google Webmaster Tools.

Google Webmaster Tools
https://www.google.com/webmasters/tools/

*Add the site to Google Webmaster Tools (If you haven’t already done so)
*Verify ownership of the site (If you haven’t already done so)
*Click the site so you can see the Dashboard for that site
*Click on [ More Details ] from the red malware warning bar
*Click on “Request a Review” and complete the form
*Wait a few hours to a day or so for the warning to be removed from the search results (IF the site is clean)
*Check your messages in Google Webmaster Tools for messages related to the status of your review

How to remove the ‘This site may harm your computer’
http://25yearsofprogramming.com/blog/20071223.htm