Fragmented files

[billwil]

hello, I have a Athlon 1000mhz system running XP, I ran the defrag program and got the results several files (10) are fragmented which defrag could not defragment. I Then ran CHKDSK at the command prompt and it came back with
" there is a problem with the file system, run CHKDSK /F,to fix the problem. I typed in CHKDSK /F and it came back with CHKDSK can not run because the volume is in use by another process,would you like to schedule this volume to be checked the next time the system starts (Y/N) , I type in Y, restart the system and the CHKDSK process works, but without doing the /F parameter and identifies that there is a problem in the file system. How do I get chkdsk to complete the /F parameter to fix these fragmented files???
I have a 120GB HD with 88% free.

the sytem uses NTSF file system

most of these files are in the Temporary Internet Files\Contents.IE5, and all have the suffix .xml and vary in size from 1 to 14K and one, the Windows update log is 1MB.