Get cleaned all the files with an antivirus tool at your PC level and then upload the files into the server. Once done, setup 755 permissions for folders and 644 permissions for files. This will help you in one way to protect your site.
If you have your own dedicated server/VPS you can install all kinds of security tools to help protect you. If it's a shared hosting account there isn't much you can do except make sure you have clean/secure code and keep it updated if using something like a CMS.