In some instances, I've seen a partition in which Windows reported the partition as severely fragmented. The partition only contained the Exchange database and no other files. So the question is, do we and can we perform a Windows file level defrag?
This answer is directly from Microsoft PSS.
"Based on your inquiry, I understand that you need to know if it is recommended to do a disk level defrag on an Exchange server. If I have misunderstood your concerns, please let me know.
According to your question, I'd like to point out that you can perform a disk level defrag on an Exchange server. However, if the disk holds only Exchange Server databases, it is not necessary to do disk-defragment because Exchange can do it internally. You may want to defrag the disk in order to improve the performance, but you may not see the result that you expected. Exchange uses and releases pages inside the database directly regardless the disk fragmentation. Exchange defragment is a file level defrag. Exchange online defragment will rearrange the data but not release the fragmentation space. Exchange offline defragment will rearrange the data and then release the free space. Therefore, the Exchange offline defragment is recommended. Anyway, you can do a disk level defrag after Exchange defragment if you want to do."
Microsoft Professional Technical Support
Useless to defrag on the File System point of View.