Take the boost pipes off, and remove the intercooler. I'm not sure about the E46's but on the E90 you have to take the bumper off. I always use Prepsol to loosen up the grease/oil in the intercooler, and leave it to work about 15mins. After that I hose the crap out of the intercooler with a hosepipe.
Afterwards, just let the intercooler stand to let the water drain and for the inside to dry out. Make sure nothing gets into it while standing to dry out. Then just refit and be safe in the knowledge that your intercooler is 100% clean and free of turbo shards/metal shavings etc.