Virtually everything under program files were skipped. I can't start re-installing of my programs. I am currently transferring all the files under program files to a new directory so I can place them back. I doubt this would work due to registries. If your applications can't be backed what was the point of even copying program files? Please, I need your advices.
The point of backing up files is to avoid losing the contents of those files if the files you backed up are lost or damaged. Backing up installed program files does not give you the ability to install those programs on other machines -- you'd need to back up the installers to do that.
If you want to back up the installation of programs on a machine, you need to use a backup program that's capable of backing up the entire installation. Acronis Backup and Restore, for example, can do that. Backing up just files won't do it.