I received an email that as a Level 1 science student, that I must apply to the Level II program that I want to be considered for the 2009-10. Could someone please explain this to me. I do not want to switch programs and I assumed that I would automatically get into the 2nd year of my program as long as I passed all my first year courses. Is there a chance that I may not get into 2nd year? Can someone please explain this email to me. Thanks in advance

you have to pick a program to specialize into.

You'll definitely get into second year as long as you fulfilled all the requirements.

They're just asking if you want to specialize or not.
For instance, if you're currently in life science you can enter the life sciences honours program, Biochemistry, Chemistry, or Biology programs (and their specializations). If you have any trouble, you can always go into the Science office in BSB to get some help with your selection for next year.