Chrome says my website contains malware?
Chrome saying while I am accessing my site, after searching I cleaned my code from the site but chrome still showing then I removed all files from my site and just upload index.html (blank file) but warning is still showing.
Answer
Chrome warnings will be based on black-lists which record where malware has been found in a site or domain, this isn't a live "scan" and does not necessarily mean that malware is on that page or at that specific time. It is not clear from your question if you've created a new folder and index.html and you are also seeing a malware warning when browsing to that URL, or if you've replaced your site content with an empty folder and index.html and that warning is still showing. Once you have taken the steps to disinfect the site then you can request a review which should help remove the warning http://support.google.com/webmasters/bin/answer.py?hl=en&answer=163633.
The malware warning should be taken seriously even if you are confident in your own site content as crackers use automatic toolkits to find vulnerabilities in websites and inject code into them to infect visitors, as these kits are largely automatic there isn't the protection in obscurity you might otherwise assume.
If you've not been able to find and fix the issue Chrome is warning about, you owe it to your visitors- and your own reputation- to take the site content down until you can resolve the problem.