How to remove a system partition in Windows 2003

Hi everyone,

I have in charge a server that runs Windows 2003 and has two physical HD:

* The 1rst disk with Windows installed and two partitions, C (with Windows Installation directory) and D.
* The 2nd disk was in the server since installation, and with a partition that is of Type:Basic, File System: NTFS and status: Healthy (System). It has another partition, E. When I installed some software, there were written some folders, which I can rename freely, so I think they are not important.

The question here is: How do I do to remove the E, without damaging the operating system, taking into account that it is a System partition?

Thanks in advance for your answers.