first question has to be why you put thermal paste on your motherboard, its supposed to go between the hsf and core on the cpu, did you put it on the northbridge chipset?
I've used a washcloth and 70% isopropyl alcohol (regular rubbing alcohol--I was too lazy to get the 90%+ stuff I should have gotten, as I've heard stuff of less purity can leave residue and stuff) with no problems.
"The first step is to clean the CPU and heatsink. I like to clean both using a solvent like miner spirits or Goof Off. Both of these will do a good job cutting through grease and gunk, especially if you're cleaning off some old thermal compound. I use a cotton swab or que tips to clean both the bottom of the heatsink and the CPU core. We only need to clean the CPU core itself. It's unnecessary to clean anywhere else on the chip, since it won't be contacting the heatsink. After I clean up with the solvent, I finish cleaning with Isopropyl Alcohol (get some good quality stuff. It should be under $5). I use a lint free tissue for this job, and clean both the heatsink bottom and CPU core again. Just let that dry off before going to the next step."
I don't know if you'll have this, but in Montreal the Transit system cards are like very thin bendable credit cards. They work really well when trying to remove thermal paste around the die. I ususally use paper towel to remove the rest on the die itself.
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