The PWM block in simulink can be used for this purpose.
The input for this block can be any number from 0-255, depending on how bright you want the LED to glow.
0 being the least bright, and 255 , the maximum brightness.
The pin in the PWM block is hte pin where the LED is connected to in yout Microcontroller.
Remember to connect a resistor in serieis with the LED.