I do not recommend cloning. Problem files can be saved and reinstalled everytime you reimage. The best you can do is do it the long way, erase the drive with multiple methods and reinstall software one by one. Can OEM or retail software have hacks built-in? Of course, but unless you want to use the ultimate hack-proof tool that is 100% effective (turning it off) then you have to fight battles you can win.
What you said about "problem files" is true, but there is more to the story. Cloning is still valuable in a backup routine.
HD Clone. Free if you clone to a larger drive (natural enough in this world of ever cheaper capacity) then run "DISKPART" (its a DOS throwback included in you windows owners platforms) to stretch the partition to the new drives full size. If you want to pay then still HD Clone, the slicker pay versions are arbitrary sizing, SCSI and dynamic drive capable. Under no circumstance use Acronis snap-deploy or other enterprise tooling unless you have money to burn or are a user of "ahoy there me hearties" software. Sledgehammer and nut comes to mind. Cloning plus spindle media image backups is good discipline if the installation in use is making money for you!