New HDD mavericks installation

My hard drive went bad so I sent it to my uncle (IT specialist) to replace the hard drive. He proceeded to install mavericks, Microsoft office , and basically hooked me up. Application wise. Before I sent my macbook, I backed up my hard drive using time machine.

My question is, is there any way to

completely restore my hard drive using time machine without losing the programs he installed ?

If not, what's the next best way to restore my hard drive from time machine?