I know nothing about it but I would think you will have to get the os specifications and assembly language requirements, then find out how to do inline assembly with your compiler. google around and you will probably find the information such as read some of these google links.
But if Linux is the OS running on your AT91RM9200 microcontroller, then there are no physical interrupts you can get access to. All user-mode programs live in a nice virtual world well away from the hardware.
Unless you're talking about a kernel-mode device driver for some new device you've attached to the micro controller in some way, in which case that's a completely different problem. One which needs a far more detailed explanation than a 1-line "help" post.
The other scenario is that your OS/Compiler you mention refers to the platform you're developing on, not the platform the code is running on. This doesn't really help either.