I did some work for a client , she made me wait almost a year to get paid and then only paid me little over half of what she owed. I have sent her lots of E-mails, and registered letters over last 16 months but she says that her "lawyer" told her it has been 2 years since I billed her and she doesn't have to pay. This is not true because I sent her a bill every month. Can I still file against her?

Did you have a written contract? She is wrong that she doesn't have to pay. A debt never expires. However, its possible the statute of limitations to sue her has expired.

Cassels Brock : Limitations Law in Ontario

This is unclear as to when the clock starts. But if you can prove that you have continuously tried to collect what is owed.