Err...
You will need at least one extra logical drive to do this. (i.e. you need at least two logical drive.)
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Set temp directory on one HDD, for example D:
Set incoming directory on another HDD, for example E:
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The files on E will be very nice & clean. Nonetheles, I still recommand you run disk utility on D every other week.
ps. always remember that it takes extra time to move file from one HDD to another. ^^