Ok to run Windows defrag on Server 2003 w/ RAID5 drives?

I have recently run into a situation where my Exchange 2000 Server has been taking a REALLY long time to back up.  And the weirdest part is that the Information Store (which is 35+ gigs) takes only about an hour or two.  The part that takes a really long time is the C:, which only has 3+ gigs of daily change.  But it takes about 6+ hours to back it up.  When I analyzed the drive with the Windows defragment tool I found something I have never seen before.  Almost the whole drive was lit up red (or fragmented).  So, after all that my question is, can I run Windows Defragment tool on a Windows 2000 Server running Exchange 2000 Server w/ a 3-drive RAID5 setup?  If not, what can I use to defragment this?  Any help in this matter would be greatly appreciated.
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Sure defrag can be run on an array.  I like diskkeeper over the built in windows tool.

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I'll second ryansoto with what he recommened about diskkeeper.

Great tool, and you get get a trial.
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