In CS6 this is done by opening all the images as layers in PS, using Edit-Align Image, then Edit-Blend Images. Then you can use software, like Photoshop, to combine the images and merge the sharpest parts of all images into a single image. Repeat this until the focus is at the furthest point. To get the entire flower in focus you would have to focus on the closest point, take a picture, then move the focus away from the camera by about 0.3 inches and take another picture. Most of these flowers had a distance of about 1-2 inches from the closest point to the furthest point I wanted in focus. In the examples I posted the typical depth of field with the 100mm at f8 at 1-2 feet is about 0.3 inches.

In macro shooting it allows dramatic increases of the normally very shallow depth of field. Focus stacking is a technique for increasing the depth of field by shooting multiple shots of the same image varying the focus from one extreme to the other and then combining the sharpest parts of each image into a single image.

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