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Before heating up the motherboard, be sure to clean the old thermal paste off both the CPU and GPU until they are as clean as the processors seen in the first picture. The process for cleaning the processors can be found here.
Lay the motherboard with the processor side facing down on the flat metal bottom of the the bare chassis (with its open side facing down) as seen in the second picture. Allow the tall USB socket to hang over the edge of the chassis so the board sits flat.
Use a heat gun on the LOW setting to heat the entire back of the motherboard for one minute. Be sure to continually sweep the heat gun back and forth across the face of the motherboard to evenly heat it.
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