Judging from one of your earlier posts, your machine is set up to boot from the cd-rom first. You should be aware that any peripherals that require special drivers as well as any video or sound drivers will have to be reinstalled. But we can cross that bridge when we get to it.
1. Insert the 98se CD in to the cd-rom drive
2. Restart the computer
3. When you see "Load from cd-rom" and "Load from hard disk" appear on the screen, be sure cd-rom is selected.
4. When the next menu comes up, select "load with cd-rom support. Watch the screen to see what drive letter the cd-rom is assigned (normally D:)
5. Type format c: and press enter. All data on the hard drive will be wiped out.
6. After the format is complete, type d:\setup and press enter. (d should be the drive letter of the cd-rom drive. If not, use the letter that was assigned during boot up)
This should do a completely fresh install of 98se.