There are couple of issues with the built-in defragmentation tool of Windows that I can think of. One is, it can only defrag the whole drive instead of a specific folder which I have mentioned on this article. Another issue is that, it eats a lot of computer resources and working on your computer while defragmenting at the same time is not advisable. This limitation is the strongest feature of Smart Defrag. The usage of this defragmentation tool is pretty similar with other defrag tools, you have to start by first by analyzing the disk before the actual defragmentation. Select the drive to defrag and hit Analyze to generate a report so you can decide what best defrag option to go for.
If you decide to use your computer while defragmenting it, then you can activate the auto pause option under Auto Defrag which pause the defrag process when the system resources go low. Or you can start Auto Defrag when the system has been idle for 5 minutes as shown below.
Another option you can make use of is the scheduled defragmentation which can run in weekly and daily basis. The result of my testing under Windows XP is pretty impressive. I was defragmenting my drive C while i'm writing this article. Smart Defrag can run on Windows XP, Vista and Windows 7.
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