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If you do it during the Windows installation you'll have the option to choose NTFS on the installation partition. You can first delete all partitions ('D' then 'L' when prompted) and leave your FAT32 space unpartitioned. Then when Windows is up you can use Disk Management in Computer Management to partition your FAT32 slice and format accordingly.
Two disclaimers, however:
1. Don't ever use FAT32
2. Don't ever use Windows.
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