You can do this by starting a new return for each of you, as seen in the image below for Online software. You will see this on the left hand side at the top of the menu once in your account. You do not need to pay for it unless you were to continue past the Review, to file it with the Canada Revenue Agency. You can later delete it, if you wish, by clicking on the little trash can beside it.

For our TurboTax CD/Download software, to start a new return, click on File at the top left corner then New to start a new return.

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I am using the desktop version. Once joint returns has been prepared (but not filed) is there a method of splitting the return into individual returns. 

Once a joint return is completed, it is in fact 2 separate returns that are being sent to the Canada Revenue Agency. You can view them by going to the detailed summary which you will find  by clicking ON the amount of your tax refund at the top left. The detailed tax summary will open on the right to be viewed.

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