I have been noticing that in the last couple months my Laptop has having an issue with overheating. About an hour ago it reached the heat limit, and shut down in the middle of 'Besieged'.

The overheating is affecting the CPU and built in GPU ... the battery is not over heating .

The laptop has been torn down and cleaned out

All the vent ports are clear

All the fans are working

My OS has had several virus and junk ware scans

The system settings are the exact same as they were in 2011 just after I bought it

What else can be causing the heat issue ?

If your 'answer' to this problem is to reinstall the OS, don't bother replying to this post.

Is this a constant issue, or only when you're really pushing the machine to it's limits? If the latter, have you actually pushed it to the limits in the past? Although I suspect this probably isn't the case, the issue could just be normal behaviour for your machine that you haven't seen earlier.

Otherwise, given everything else you've mentioned (and ignoring OS re-installation, which can sometimes clean out some stuff your virus and junkware scans may have missed) you're really only left with environmental factors (which you likely would have noticed) or hardware problems.

The system settings are the exact same as they were in 2011 just after I bought it

Unlikely.

For one thing, that game was released just a month ago. You installed it after 2011. So that's different.

For other things, you've likely installed a long list of OS updates, malware definition updates, and additional software. You've got newer drivers. Those are all different. Any of them could have changed access patterns or system load, increasing temperatures.

It could be that your four year old laptop is starting to show its age. Everything mechanical breaks down, fans spin slower, drives run hotter, vents and filters get clogged (although you said you cleaned them), some cheaper thermal pastes break down, case seals break down so air flow becomes different, and so on. Sadly everything in the world breaks down with age.

Environmentally there are also many possible changes. Temperature around the vents can make a difference, airflow around the machine can make a difference. Differences in ambient air temperature and humidity can make big changes to computer temperature. Keeping your laptop on a cluttered desk can restrict airflow more than having it on a wide open area. Etc.

Simplest view: New, untested, prerelease game is overheating your computer. Report that your computer overheats when playing the game.

I've had bad luck with laptops overheating (even just watching Netflix!). It seems to be a common problem, especially in the <$400 range. At least three past laptops had that problem, though none of our equally-cheap newer ones do - hopefully the industry has made progress on that front.

Is the laptop in near-constant use for three or more hours at a time? Try to give it a break and let it cool off. Maybe you need a cooling pad? Cheap cooling pads break alot.

In some videocard control-software you can explicitly tell the fan to run at a higher rate - I don't know if that's a bad idea though.

Personally, my family just give the laptops a ~20 minute rest when they were running hot, and used flat books to elevate the laptops (so any blankets or clothing don't block the vents), and made sure the videocard side of the laptop was resting off the edge of the book so the fans on that side could vent freely. The two (three?) cooling pads we bought both broke after a week or so (we only spent $10 on each one, so I guess we got what we paid for).

Does it make any loud noises? My previous desktop's discrete GPU had a problem where the grease around the axel of the fan kept evaporating. So I had to routinely re-oil it with machine oil every 3-6 months (depending on how videogame-active I was during a month), otherwise the fan axel would have too much friction, slowing it down, and not pulling enough heat off the videocard.

I've had this problem too, when pushing my hp to its limits. It wasn't a cheap laptop but is now showing its age a bit as it's almost 5 years old.

You could do what I did - buy an active cooling mat from a good brand name with fans it it powered from USB, and take a vacuum cleaner to the air vents while the laptop is powered off and unplugged to clear out any dust blocking the vents.

Failing that, open it up and carefully use compressed air on the cooling components and ducts.

Good luck!

Edit: also, installing thermal monitoring software to see if what you've done is having an effect helps too. There are lots of free monitoring apps available online that measure temperatures and fan speed of hard disk, cpu, gpu and case. For me, it used to bomb out when transcoding video whilst watching YouTube in HD and compiling my game. You could see the difference in the temperature graph immediately.

You're lucky, at least your CPU is overheating due to pushing it. My laptop is a 2006 Compaq Presario with Crunchbang Linux installed and the CPU runs hot while watching Youtube videos. Doing other things my CPU spikes at ~20%, but watching YT vids makes it spike 50%+.

vacuum cleaner

I heard you shouldnt use a vacuum cleaner to clean computers because a lot of static electricity can be generated, possibly destroying some delicate electrical components.

my note never shuted down due heat, but it does start to lag. When playing graphic intensive games I put stuff bellow it to rise it from the table (caring to not block any fan). It solves the lag.

Use softwares that display the temperatures and see if rising the note lowers them (its instantaneous to me).

You can put the graphics configuration on the lowest to see if its the cpu or gpu that is heating (or did you mean both are heating together?). Or, if you know where they are, simply putting your hand on the note you can tell which side is burning (I can feel it on the keyboard).

I think I bough mine in 2008 : https://www.google.com/search?q=gateway+p-7908u+fx+edition+notebook&safe=off&biw=1440&bih=775&source=lnms&tbm=isch&sa=X&ei=tBfqVL7MFPOAsQTE_4CIDg&ved=0CAgQ_AUoAw

Also, you can use brenchmarking softwares to force cpu or gpu, and figure out which one is heating.

vacuum cleaner

I heard you shouldnt use a vacuum cleaner to clean computers because a lot of static electricity can be generated, possibly destroying some delicate electrical components.

Yes, definitely never ever use a vacuum cleaner directly on or close by to components, use a can of compressed air for this at least 12 inches away from any sensitive parts.

A vacuum cleaner is OK held at a reasonable distance from external vents, say a couple of inches.

I speak from personal experience but usually you can just reach in with tweezers and pull out huge dust bunnies from an external vent on old pcs and laptops :D

Since is is an old laptop, you might consider trying new battery, or power transformator plug. You may have damaged resistors causing too much voltage on chips.