Yes you can use a CD R. Most people just use a usb flash drive or download it from the internet.
Microsoft Security Essentials is not that good of antivirus. I would say avast is better for free antivirus, which are still lacking compared to the paid options like Bitdefender or Kaspersky.-
If the pc is already heavily infected then MSE is not going to do much. You will need malwarebytes to clean it.