There are two steps you need to take.
First, you have to secure your website.
Then you have to go into damage control and try to restore your website's ranking in the search engines.
To secure your website you need to start by changing ALL passwords - particularly ftp but also change anything that requires a password in order to access. Then you should run a scan for trojans and other viruses to make sure nothing is infecting the server. Next you need to check your files and webpage code to make sure that nothing malicious has been added by a hacker.If you have a large site then this will be time consuming but it needs to be done.
Removing Malware & Securing your website
Google's Advice for your Situation
After all this is completed and you are sure that your site is malware free - you need to restore your website in google's ranking and Bing and the other search engines.
This website will help with that.
Google Webmaster Central Blog Entry
Remember that once you have completely secured your website, you need to request a review from google through the webmaster tools control panel.
I hope this helps