The Predesktop Area is part of the HPA (Hidden Protected Area). The HPA is a special area on your harddisk, usually hidden to partitioning tools. It includes all the software and data needed to recover the preloaded state of the ThinkPad. The HPA also includes some diagnostic tools and a (MS Windows only) backup tool.
The PreDesktop area was introduced with the R/T/X 40 series of ThinkPads and is present on the preinstalled harddisks of all ThinkPads shipped by IBM since then.
How to remove it
There's a BIOS setting in my T42p. After disabling the Predesktop Area, it's possible to remove the partition with standard tools. i.e. fdisk, mkfs, ...