Most of the issues that are different in written Canadian English to American English are the same differences that crop up in British English, with some exceptions.
Big one: -or/-our
eg. labor/labour, neighbor/neighbour, etc.
-er/-re
eg. theater/theatre, liter/litre, center/centre
-ize/-ise
eg. organize/organise
Especially with this last one, most Canadians don't know the proper difference themselves.
One issue where we differ from the British:
certain vocabulary:
jail (not gaol), tire (not tyre), airplane (not aeroplane).
I think there might also be slight punctuation differences with commas, but I'm not sure.
If you have a decent word processing program (eg. a recent version of MS Word or WordPerfect), I would set the language options to English (Canada) and it should help you find most things.
May I ask what you're doing that you need such translation? It seems kind of odd, as, as jphector says above, Canadians have no problem understanding US English and vice versa. Only issue would be if you're in publishing, in which case you might want to look into getting your hands on some of the stylistic manuals, such as the Canadian Press style guide. It is most likely going to be easier for you to just learn the individual rules and differences than to rely on an automatic translation tool.
Hope this helps.
Catachrest
