Yes. When you boot to Windows installation, it will ask you where you wan to install to and will show you the existing partitions. It will show C: and D:. You will need to delete C:, then choose that Unpartitioned Space to install to.
Our old Poweredge1800, win2k3sp2, has a perc raid with 3 drives. The machine stops booting at acpitabl.dat. I've booted into the recovery console from the CD, and chkdsk shows unrecoverable errors on C:\ I've been unable to even view a directory of C:\Windows, so I'm guessing that's where the errors are. Here's the nut of the problem: I need to copy some directories off the D:\ partition to an external USB hard drive. We have NO good backups of these particular directories. It's quite irritating that Recovery Console doesn't let me access anything below D:\. Is there a known procedure for: 1. Re-installing or repairing the C:\Windows\ directory, WITHOUT damaging the D:\ partition, or 2. A bootable CD image that will allow access to the D:\ drive. I know, I should have backups, and I do, for most things. These files were just updated the day before this system took a nose-dive. 
PowerEdge1800. Can I re-install Windows without Screwing Up D: Partition?