As far as I know, the only way to have marks removed from your transcript would be to fail to maintain the minimum cumulative average of 3.5. In this case, you would not be allowed to continue at Mac, and you would have to re-apply. It's only then that if you get in, you start with a clean slate.
Other than that, I'm not sure if there's any way to have marks removed. But when in doubt, go speak with an academic advisor. Hope this helps!
http://registrar.mcmaster.ca /calen...-13/pg124.html