Command to remove malicious code:
#grep -lr --include=*.php "eval(base64_decode" /path/to/webroot | xargs sed -i.bak '/eval(base64_decode*/d'
If above command gives you correct output, execute following command to perform actual cleaning:
#grep -lr --include=*.php "eval(base64_decode" /path/to/webroot | xargs sed -i.bak 's/<?php eval(base64_decode[^;]*;/<?php\n/g'