You've received some great advice so far. Here would be my tip, if you don't mind re-shooting your photos.
Pick the flower and then take a picture of it against a contrasting-colored background. So, if your flower is a beautiful, bright pink, take a picture of it against a white background or if it's a soft, light color, take a picture of it against a black background. Like Liz said, use the macro setting on your camera if you have one and try the best you can not to use the flash (that way you won't have strange lighting on the extracted flower and you can create your own light source once you get it extracted onto your layout).
That's my 2-cents
