Removing 98se

Edit c:\boot.ini to remove the entry or use MSCONFIG to remove it.

Windows 98/XP dual boot
Boot to XP; go to control-panelsystem-folderadvanced tabstart-up/recovery button.
Set default OS to boot = XP; also there you can edit out (remove) the reference to '98 (typically c:windows).
Now locate/delete the '98 (c:windows) folder from the c: (Primary) partition; delete the bootsect.dos, msdos.sys, io.sys from c: root; delete the '98 swap-file (typically WINA20.386) from the c: root. Any other unwanted folders too (in C: ) can go - as long as you don't remove the i386 (for XP) if by chance it ended up there...
Critical files to be sure to leave in c: root are:
ntldr/ntdetect.com/boot.ini/Page-file.sys (if it exists there).
Reboot and you should have only XP as an OS to boot. Once happy that XP is OK, empty recycle-bin, defrag drive to tidy up the scene. Job done.
You now have a Primary partition (fat32) - you don't say how large it is... - that "can" be used for data, or you 'could' use System Commander (rather than Partition Magic - PM has some known/reported problems with XP..) and reduce size of Primary to around 100Megs or so (if it's on "the large" size...?) and expand XP (Extended?) partition to absorb the space?

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