Why would it be mounted towards the top of the case ? That's weird because that's where hot air resides (hot air being lighter than cold air... it rises to the top of the case).
If you cannot move the hard drive away from the case's compartment then you can take a look here
for a hard drive cooler (hoping it fits since there's only 1/4 inch above the HDD).
One other option to installing a cooler directly on the HDD is to install one to cool all the drive bays.
Check this one by Thermaltake
(as with everything else... make sure it fits in your case before buying it).
While designed for the Thermaltake Armor Case, the iCage is compatible with any ATX case with three consecutive open 5.25â€ bays.
If I'm not mistaken HDDs are safe until 60C when operating. But that's way too high a temperature ! Just like an Intel Prescott is safe while below 65C it doesn't mean you should run it at 64C all the time.
Even 39C is a bit high mate. You should try to keep it below 32C as it will help prolong your HDD's life. I think your major problem is the HDD location within the case (being at the top).