Inspect the plant in the morning when the flowers are open. Identify which flowers are male and which are female -- female flowers are located on the actual zucchini, as the vegetable literally grows out of the blossom. Although you can harvest both the male and female flowers, male flowers are larger and easier to stuff with food items, such as cream cheese.
Sever the female blossom from the stem of the zucchini fruit with a sharp pair of scissors or knife, when the zucchini is about 2 inches long. Cut male flowers from the vine about this same time, when the actual zucchini on the plant reaches 2 inches long, and before the flowers start to turn brown, which usually takes about a week. If they are left to sit on the vine too long, they will start to wilt and die. Leave the base on the flower and cut at the point where the flower's base and the plant's stem meets.
Place the flower and its base in water.The base is the part of the flower in which the blossom grows from and is located directly underneath the blossom. Both the blossom and the base should sit in the water to keep the flower hydrated and healthy until use. Leave the flowers in the refrigerator until you are ready to use them.