Not directly related to your question re how to remove malware, but consider this - I'm guessing you're seeing Google's red "The site ahead contains malware" alert, which is, admittedly, alarming; however, this alert is not in real time. In other words, this alert shows up for websites that were once upon a time infected when scanned by Google, even if the site has since been cleaned up.
If you have a Google Webmaster account, try resubmitting your site to be tested by Google for malware. If it still reports that your site is contaminated, then yes, be alarmed; however, there's a good likelihood that the alert will go away, because you actually were already successful in removing the malware from your site.