Hard to evaluate because of the low resolution and because it is underexposed. However, it looks to me as though a lot of the image is out of focus.
The trick is two things: finding the nearest and farthest points, and figuring out the amount of focus difference that will not leave anything out of focus. Helicon remote allows you to set the near and far points. I used it only briefly, but with my equipment, I found that its default focus changes were too large, and I had to adjust it to give me closer focus points. I now do it by hand. I don't know how large (front to back) this flower is or what magnification you have, but if it is anything close to 1:1, my guess is that you will need considerably more than 3 shots.
Russell, in case you're interested in an ID of the plant, the photo appears to be Queen Anne's Lace, also known as wild carrot in the midwestern US. The flower cluster begins as a ball, that unfurls into a relatively flat grouping of many short flower stalks.
A re-proccessed by Cogito https://g2.img-dpreview.com/518B7E52...0F1BFA173C.jpg
?
And since I'm here in question-posing mode, since you used Helicon remote, is there any reason why you didn't use their stacking software and compare with the same shots stacked in AP? Or better still, take DanK's advice and redo with more shots in the stack (or stacks if you try the Helicon program in addition to AP).
Hi, Yes there is a reason I didn't use Helicon Focus, I only had a years license for it and as I was not 100% sure about changing and going down the flower photography road so I didn't renew it. I am also waiting on two soft boxes that accept E27 bulbs as I also want to use continuous light rather than flash. Will get another image/s up as soon as I am setup. Thankyou for the reply. Russ