I asked about this a couple of months back.(looks like it's pass the purge date)
The microfly and most SFF cubes have a 3inch or 75mm vertical clearance opening for the MB tray. That usually limits you to the stock cooler or other down-blowing HS types(zalman or TT flower orbs) if you want to be able to slide the tray in and out with the HS in place. Or you can use a TR SI128 type and mount the fan after the tray is in.
-Zalman also makes the CNPS 8000 specifically for this application.
-TR makes the MST-9775LE for this as well
-hardware logic seems to think the Silverstone NT06 CPU will fit w/o the fan.(probably works better in the TT lanbox where the psu fan draws air up thru the HS.)
On the microfly the PSU isn't located over the cpu, so there is enough vertical clearance for tower types like the TR ultima90, but the structural rib on the cpu side of the case blocks it so you'll have to dremel it for a tower to fit. (Somebody did this with a microfly and an ultra120, I think. dont have the picture link anymore.)