Well, I am not really sure this is going to be worth doing, but it is possible. Suppose you had your \Documents and Settings on drive D.
1) Run a commandline,
JkDefrag -f 0 -a 6 D:\* -e "D:\Documents and Settings\*"
and wait for it to terminate.
2) Run a second commandline,
JkDefrag -f 0 -a 3 "D:\Documents and Settings\*"
3) Preferably, run a third,
JkDefrag -f 0 -a 3 D:\*
Well, that's too much work, isn't it?
Jeroen the author of JkDefrag is now putting together its ver 4, which is to come with a scripting system to make micro-managed defragmentation possible.
I am looking so much forward to it!