The very important thing is to lower down the cpu clock first.
The second important part is to verify there is no physical cooling problem (like dust on the fans, cat or dog hairs in the heatsink ect)
On most computers, the fan speed is directly operated by the bios or the os automatically.
The cleaning/lowering cpu speed process should let the cooling performs better, and, if the T° goes down, so the speed of the fans too.
If it's not, I advise you to look into
It's a little application that uses
pwm is the thing commonly used to drive the fan rotation speed from the computer, see: https://secure.wikimedia.org/wikipedia/en/wiki/Fan_control#Pulse-width_modulation) to regulate automatically the fan speed according to the CPU temperature
Here is little documentation about it: http://www.lm-sensors.org/wiki/man/fancontrol
I assure you that is more easier than it looks, but primary you need to install and configure sensors to your computer.
It has a little easy-config script to help you to detect & configure your sensors and stuff, called
sensors-detect in most distros.
I advise you to google about it, including your distro name and your laptop brand/model to find the best settings
After that, just run
pwmconfig as root.
It detects driveable fans and temperature sensors, and asks you Min/Max Temps for cpu and Min/Max fan speed you want.