then you have a problem.
You've likely "smudged" the thermal grease. In which case I'd advise you starting over.
Buy a cleaning kit:http://www.newegg.com/Product/Product.aspx?Item=N82E16835100010&cm_re=thermal_paste_remover-_-35-100-010-_-Product
I've used that several times and have been happy with the results. Just follow the instructions and it's easy. In the end you'll have a factory clean surface ready for new thermal grease!
Next you'll need some new thermal grease. Used this on 4 CPUs and it's been outstanding. http://www.newegg.com/Product/Product.aspx?Item=N82E16835100007&cm_re=thermal_grease-_-35-100-007-_-Product
After you've removed all the old grease and cleansed the cpu surface you'll want to apply the new grease.
1. Place 1 to 2 drops (it comes out like a poop, think small turds) on the cpu.
2. Use a Credit Card or Drivers License and spread the grease as thin as possible over the entire cpu plate. You want to go as thin as you can manage. The less grease the better. However if you can't cover and area squeeze out a tiny grease poop and then shave the excess off with the credit card. Less = More.
Your all set. Install the cooler normally.
If your getting CPU temps at idle over 45C something is wrong, likely there wasn't a good seal between the cooler plate and the cpu. If this happens just shut down and repeat the above steps and try to use less thermal grease.