Bring a large pot of lightly salted water to a boil. Cook macaroni according to package directions.
While the noodles are cooking, in a large deep skillet melt the butter and then sprinkle in the flour. Whisk together over medium heat. Be careful not to burn the mixture. Cook for about 2 minutes while whisking. Pour in the milk, a little at a time and whisk until smooth each time. Cook the mixture while whisking until it has become very thick. Add the smoked Gouda and cheddar cheese and stir until melted. Stir in mustard, salt, pepper, and Cajun seasoning. Remove from heat.
Drain the macaroni noodles. In a large bowl mix the noodles with the cheese sauce. Top with green onions.