Hey I am taking Bio 4C09 which is the senior thesis. Bio 4F06 is a smaller project, but similar in structure. I keep hearing that the difference is that 4C09 tests a hypothesis, while 4F06 doesn't necessarily. I just consider it a smaller project, where 4F06 doesn't have to be a full out study/experiment -- it can be a large lit review..? Not sure about this though.
To get into this course, you must print out the permission form from the Biology website (on the left menu, click on Undergraduate Studies>Permission Forms>Bio4C09/4F06). You need to find yourself a supervisor and (maybe?) a co-supervisor who will be willing to watch over a project. I'm not sure if you need a co-supervisor for 4F06. You also do not necessarily have to come up with your own project, but choose supervisors that you are interested in working with based on their research interests, which you can look up on different departmental websites.
For details about the course, check out the course outline for Bio 4C09/4F06 here (click on 400-level course and "Bio 4F06"):
http://www.biology.mcmaster. ca/ugrad_cours.htm