Sometimes I cut out a disk of fondant a little smaller that the top of the cake and the same color as the cake-or a contrasting color. (I ice my cakes in buttercream.) I attach any bows, figues, etc. to that disk and set it on top of the cake. I can easily life it off when it's time to cut the cake. Maybe that would work with your flower topper.
Here are some examples:
http://cakecentral.com/gallery/1902801
http://cakecentral.com/gallery/1593784
http://www.flickr.com/photos/hjscakes/
Silk flowers...I think I would do as Debi suggested.
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