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do i have to take out the full motherboard if i want to refresh the thermal compount, or just the Cpu cooler

If you can clean it while inside the case then of course you don't need to remove the motherboard.

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you should only have to take the cooler off to apply new thermal compound

 Motherboard - Asus Z97-WS ll Processor -Intel i7-4790K ll Cooling- Custom Loop ll RAM - Corsair Dominator Platinum 16GB(2x8) @2400 ll Graphics Card  - EVGA GeForce GTX 980 TI ll PSU - Corsair AX 1200 Watts ll SSD - Samsung 840 Pro 256GB ll HDD - seagate barracuda green 2TB & Seagate 4TB ll Case - Silverstone TJ11 ll Audio - Asus Xonar Essence STX  ll OS- Win 10 PRO 64-bit ll Keyboard- CM Storm QuickfireTK Green Switchesll Mouse- Logitech G502

  

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yes but i think it will be hard to delete the compund which is there for about 3 years

It shouldn't be.

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99% isopropyl wipes will get that stuff right off.

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I wouldn't take the cooler off before turning the computer on for a bit, to warm the paste up so when you take the cooler off the cpu doesn't come up with it.

 Motherboard - Asus Z97-WS ll Processor -Intel i7-4790K ll Cooling- Custom Loop ll RAM - Corsair Dominator Platinum 16GB(2x8) @2400 ll Graphics Card  - EVGA GeForce GTX 980 TI ll PSU - Corsair AX 1200 Watts ll SSD - Samsung 840 Pro 256GB ll HDD - seagate barracuda green 2TB & Seagate 4TB ll Case - Silverstone TJ11 ll Audio - Asus Xonar Essence STX  ll OS- Win 10 PRO 64-bit ll Keyboard- CM Storm QuickfireTK Green Switchesll Mouse- Logitech G502

  

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but i think the paste is fine but i still couldnt figure out why our desktop pc is so slow

Viruses, but if you choose to replace the thermal compound, make sure to let the computer run so that it's easier to take off the thermal compound off.

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run ccleaner and malwarebytes and your preference of antivirus (I like avast) or if it's that bad save all your data you want from the computer and do a fresh install.

 Motherboard - Asus Z97-WS ll Processor -Intel i7-4790K ll Cooling- Custom Loop ll RAM - Corsair Dominator Platinum 16GB(2x8) @2400 ll Graphics Card  - EVGA GeForce GTX 980 TI ll PSU - Corsair AX 1200 Watts ll SSD - Samsung 840 Pro 256GB ll HDD - seagate barracuda green 2TB & Seagate 4TB ll Case - Silverstone TJ11 ll Audio - Asus Xonar Essence STX  ll OS- Win 10 PRO 64-bit ll Keyboard- CM Storm QuickfireTK Green Switchesll Mouse- Logitech G502

  

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