defragment windows Small Business Server 2003

In installed SBS 2003 and ran the defragment utility.  After fininshing the summary says "some files could not be defragmented"  About 50% of the files are still showing as red(fragmented).  Should I run the utility from safe mode?  Or, how do I defragment the rest of the drive?  Thanks.
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Lee W, MVPTechnology and Business Process AdvisorCommented:
What files are showing as fragmented?  If they are particularly large, MOVE them off the drive.  Then defrag the drive, then Move them back.  That would be considered a MANUAL defrag.

Otherwise, there are programs available that do a MUCH better job than Windows built-in defragger.  Maybe some free ones too... though I've usually used Diskeeper.
Shreedhar EtteCommented:

Refer this article:

Hope this helps,
My suggestion for a good defrag program is this:

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