How can I clean the heat exchanger on an intertherm m1mb090bw gas furnace. I have vacuumed it out from the top where the pipe attaches and also from inside the fire box but it is still restricted.

Why you think it is restricted? If it is true you can use a compressor, firt of all, buy you a good protection mask and safety glasses, cut the power and gas to your furnace and blow air into the burners holes. Also blow from the other side near the connection to the exhaust. Be careful with wires and other elements. Good luck.