Battle Encoder Shirase 
BES is a small tool which limits the CPU usage for a specified process: for instance, you can limit the CPU usage of a process which would use CPU 100%, down to 50% (or any percentage you like). With this, you can use other programs comfortably while doing something CPU-intensive in the background. By limiting the CPU load, you can also cool down your CPU immediately when it happens to get too hot. Of course the processing speed will slow down proportionally if you limit the CPU usage, but it should be much better than crashing because of heat or (in the worst scenario) having your computer broken with a burned CPU.
Furthermore, BES can hide any windows you don't want to be seen for some reason, without killing the process, and restore the hidden windows again anytime you like. 
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