Iframe Trojan / Virus of Alcobro.net

Hello! We have a big security problem. Website of a friend is infected with iframe code from alcobro.net. Every .php, .html, .htm, .js file has an iframe code at the end of file. Norton can find infected files but cannot repair it. They are more than 1000 files. Too much to clean manually. I need help to clean these files because there is no clean backup. And I must be sure that .swf files are not infected.