Ok follow the steps........
1.Boot into windows 2000 and go to system properties

Advanced

Startup and recovery and choose windows 2000 as a default operating system and uncheck display list of operating system for 30 seconds........now u can't boot into win 98
2.Now if u have windows 98 boot disk or floppy....boot throght it.......and choose start computer with cd rom support option and on the command line type ur floppy drive letter or cd rom letter...... Example "a:" and then press enter if u have floppy and if ur CD letter is "g" type "h:" and hit Enter...............Then type "format c:" and label it as DUMP or whtever.....
OR I think u can also format with in the windows just right click which drive to format and then click format .
Restart now you have single OS and ur c: drive is formatted........