If you have a stamp postitioner like the SAMJ, you can ink the stamp with the flower colour and then use a damp Q-tip to remove the colour from the stem. Stamp, thoroughly clean stamp and then ink the stem area with the green, again using a Q-tip to remove any that has got onto the flower part. I've done this very sucessfully with stamps like the tree from Thoughts and Prayers.
If you check the tutorials on Masking in Resources you'll see how to use post-its to mask off a whole image, you can also do this with just part of an image - but whether you can use that technique or not will depend on how the stem is positioned relative to the flower.
Splitcoaststampers - Masking Basic Technique Tutorial by Beate Johns