Right, When you boot with your Vista cd. The install process will detect your hard drive. You'll then be able to delete the linux partitions. On the unpartitioned space, you can either select to install or create the partition either way the windows install will format the partition for you to NTFS then it will begin the install process.
Here's what you would look for.
You'd select your linux partitions and click delete. You would then see a unallocated disk like below. Here you can select next or format.
You dont have to "put" NTFS on the disk.. It's the type of formatting you do. Windows Vista Install will do this for you.
Just like you can format a disk to Fat, Fat32 or NTFS.