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What (Windows app) can I use to defragment FAT32 directories?

I used to be a fan of PerfectDisk, but they've disabled the feature in their latest versions, and I have drives that I need to use both in Windows XP/7 and other OSes.

I've checked or tried these ones:

  • UltimateDefrag
  • UltraDefrag
  • JkDefrag/MyDefrag
  • PuranDefrag
  • Defraggler

None of them handle FAT32 directories. So, what can I use?

share|improve this question
People still use FAT32? :) – Earlz Aug 15 '11 at 22:09
AFAIK there's nothing simpler for an external disk that needs to work on any OS – TheNewbie Aug 15 '11 at 22:14
By "boot time" do you mean pre-desktop time, i.e. the commandline-like interface that boot-time chkdsk runs from? – Aug 15 '11 at 22:38
Yes, it's the only moment when directories in FAT32 can be defragmented (the same limitations exist with MFT+etc for NTFS drives) – TheNewbie Aug 16 '11 at 0:19
You said Defragger, but what about Defraggler? – user3463 Aug 16 '11 at 2:25

IoBit's Smart Defrag 2 has boot time defrag.

share|improve this answer
Thanks, I installed it. But it only handles files like 'pagefile.sys'. Directories are not defragmented for FAT32. – TheNewbie Aug 17 '11 at 0:54
It has an auto defrag feature that defrags during idle time. It can be turned on for any drive. – Kevin Aug 17 '11 at 1:32
Yes, but since the fragmented directories are spread all over the partition, it doesn't achieve too much. I meant that at boot-time, it only handles files like pagefile.sys, not the directories, which I'm trying to defragment. – TheNewbie Aug 17 '11 at 10:41
Since directories can be defragged while Windows is running. I do not understand why they would need to be defragged at boot time. There are "Deep Optimize" and "Fast optimize" options when defragging. Perhaps they can give you the result you are looking for. Of course if the drive is too full no defragging program is going to work. – Kevin Aug 17 '11 at 12:45
Directories cannot be defragmented for FAT32 drives, unlike NTFS drives where the only files that cannot be defragged "online" are the MFT, metadata, etc. I guess your FAT32 thumb drive just wasn't as fragmented as my external HDD, or you'd seen what I'm talking about. – TheNewbie Aug 18 '11 at 18:57

How about Window's built in Defrag tool?

You can easily set a script to launch it on start.

share|improve this answer
Mind putting the contents of that script here? – soandos Jul 15 '12 at 19:01

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