this mean that i can't use arduino's librairy to program my microcontroller ?
No, it doesn't mean that. It means that you need to be up front about the fact that you do not have an Arduino, and that the IDE you are using is not from Arduino.
Interrupts are not library features. You may, or may not, be able to use Arduino's interrupt code. I would guess not, as interrupts are pretty much hardware dependent and you hardware is a lot different.