1) Lock down your site by using an .htaccess password so your customers are not attacked by the hackers code.
2) FTP all of the files to your local machine and use a program like WinGrep to identify and remove all malicious and anomalous files containing hacker code. Look for keywords such as 'base64','eval','decode'.
3) Delete the files on your hosting account before uploading the clean files.
4) FTP the clean files back to your hosting account and read and implement the security patches and contributions found in these two threads. Admin Security and Website Security.
5) Change all of your passwords: FTP, CPANEL, STORE ADMIN and DATABASE
6) Make sure File and Directory Permissions are set correctly. Directories no higher than 755, Files no higher than 644 and the TWO configure.php files no higher than 444
7) If your site has been 'black listed' as an attack site by Google, then log into Google Webmaster Tools and submit the site to be re-indexed and verified to be removed from the 'black list'
8) Remove the .htaccess password protection so your customers can resume making purchases from your website.
9) Monitor your website using the newly installed contributions to prevent future hacker attacks.
10) If you feel you can not perform any of the above steps, you should seek professional help to ensure all malware is removed.