..........most of the times the CPU usage is 100%!!!
This indicates a probable software related problem. Two many programs running at start-up, a poorly written program hogging CPU time.
Lap top coolers are pretty good to keep a healthy properly running lap top in a cooler running condition. How ever if their is a thermal related problem then they only prove to be band-aids\temporary fixes. As you noted, you got the cooler because it was getting hot, it helped
for a while but the problem has returned. Actually it never left, and has gotten worse.
After following the advice given then I feel it is time to check your running processes and try to trim them down.
You also said you know you are not infected. The symptoms you stated, 100% CPU usage, points to to the contrary, perhaps