Backing up sector-by-sector System partition only

I have a large 1TB disk with a small (40Gb) Windows system partition "C:" and the remaining 960GB or so is used for an extended (Data) partition "D:". I want to backup sector-by-sector the system partition "C:" (plus MBR) only and do not want to include the extended partition "D:" in the backup. But, my ATIH2011 either does not allow a sector-by-sector backup of one partition or even if it does, then it cannot restore it. When attempting to restore, it says something like: "Not sufficient space ...bla-bla....." (While there is plenty of space). If doing a NOT sector-by-sector backup/restore, then there are no problems.
The reason for sector-by-sector partitioning is to backup hibernated Windows along with hiberfil.sys