This is why I pointed out that often certain files themselves will be found to be the fragmentation rather then the drive overall. After defragging the drive and seeing fragmentation rather high you have to start looking at specific files that simply can't be defragged.
Are you storing a large number in any one folder? music, video, updates, etc.? Regardless here's 4 tips on how to lessen the effects of fragmentation.
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1. Defragment early. When you set up a new hard disk drive, whether as a data drive or as a new system drive, defragment it as soon as the first wave of installing applications, copying data, etc. is done. This allows the defragmenter to do a fair amount of work while there is still plenty of free space on the drive for that work to be done.
It also allows for some key file system structures to be written out in contiguous order, such as the swap or paging file, or the file the system uses to hibernate the computer. (Note: These files can be deleted and recreated if needed, but few people are in the habit of checking to see if they need this done, or doing so.)
2. Free some free space, or add some. If you're using a hard disk drive that's more than 75% full and remains that way consistently, it will be that much harder to do anything about existing fragmentation. Either move some stuff offline or upgrade to a larger drive.
If the drive itself is more than a few years old, odds are you'll be able to upgrade to a model that has at least twice as much storage, a faster bus type, faster rotational velocity and bigger on-board cache—all at the same price you paid for the original (or even less). All these things help offset any degradation of performance due to fragmentation.
3. Add more physical memory. Adding memory to any computer improves its performance across the board, including how well it deals with fragmentation. In general, if there's more memory, the system can devote more memory to caching hard drive access, and the overall effects of fragmentation are further diminished. Memory is cheap enough now that it makes sense to add a fair amount to start with. I'll pay off one way or another.
4. Do defrag, but not to excess. Set up a disk defragmentation schedule, but do it only when the process of disk defragmentation is not going to hobble performance—i.e., when you're not actually at the computer (or server) in question, or during a period of low system activity. Defragging more than once a week is pointless; the time spent doing the defrag far outweighs the benefits gained, especially if you do it that obsessively. "
http://searchwincomputing.techtarget.com/tip/0,289483,sid68_gci1216429,00.html
That's a continuation of a 2006 article
New hard disk drives reduce need for disk defragmentation seen at
http://searchwincomputing.techtarget.com/tip/0,289483,sid68_gci1216336,00.html#