Probably you remember a great tutorial on programming external interrupts of AVR microcontrollers from Protostack. So here it is – next one on programming timer interrupts. In this particular case tutorial covers ATmega168 and similar AVRs. But techniques may be applied generally to all AVR MCUs.
To be specific, write out covers short intro to timers and then leads to examples of several modes of operation including 8 and 16 bit timers. Examples are given in C language that can be compiled with AVR-GCC compiler. Hopefully you’ll find some good start in using them.