They are soft green scales, and some of them appear to be parasitized (the darker ones). The ants "farm" them, feeding on the honeydew produced by the scales. The ants also fight off parasites and predators of the scales. At least in Florida, control of the ants by treating at the base of the tree will usually be sufficient, because as soon as the ants are gone, the good guys move in to eat all the scales. I assume that will be true in your area as well.

I agree, ants are not your friends. They farm pests like aphids too and can even carry desease from other trees. That and encouraging the good 'ens are the right action.
Additionally the answer to many infestation problems is simply to make the tree healty. First and formost and way ahead of the next 3 combined is mulch. A good mulch AT LEAST 6 INCHES THICK or More will really make a citrus feel like it's living right. Citrus like to have shallow roots for feeding and this gives them a happy, cool, moist, nutrient rich envoronment for those feeder roots.
Mulch will decompose and feed the tree, but that also means you have to replentish it every so often. When the mulch gets down to less than 5 inches, dump lots more on it. To start you may want to use a good compost at the soil level, but after that, or on top of that, just about anything will do. Lawn rakings, old or moldy hay are good. I actually get a tree trimming company to pay me to let them get rid of all that mulch from their chipper truck. (er uh trash as they call it). The dump charges them $45 so I ONLY charge them $30. and laugh all the way to the (soil) bank. I'm a little cautions of kitchen trimming that come from the grocery as I don't know what kind of bugs they may carry.

When I look under the mulch under my 100 citrus trees, there is a beautiful rich black soil. It's a site to see. I don't have any pests, or other problems. Just rich green trees with delicious fruit heavy on all the branches.
(sigh) I get all silly just thinking about it! lol Think I'll go make a fresh squeezed tangerine juice, or maybe a limeaid!

"Citrus grows and produces best with no amendments to the planting hole, and without mulch. It will also have the least problem with lower-trunk diseases if not mulched. But if your goal is organic production, you may need to use such things. In that case, yes, keeping a ring right around the trunk clear will help. As for mulch depth -- I don't know. My recommendation is no mulch at all." Found by citrus form search help quote said by Mr. Doctor Manners

So based on what you saw (pics) what is the recommendation
This is what I think of doing

1. Prune the infested branch and control the ants
2. Control the ants and leave scales on infested branch. Then nature takes care of the scales

If I am the one who has that problem, I would control the scales first so the ants have nothing to farm for food. Scales are hard to control if you picked them one by one or by using alcohol and swabs. I have seen thousands perhaps millions of scales in my sister's trees. Just too many. I hope that don't happen to you. Sometimes you need drastic measures to control them.
Many times the good guys are not around to help or not enough of them.
It depends on your situation. It's your call.

I control scales by using a brass adjustable nozzel on the end of a hose and turn it to a forceful spray. It knocks them off very easily.

My sister's scales are different- brown in color and pretty big too as large as dimes if I remember right. Very very hard to scrape them even with a knife off the bark. They looked like were almost part of the bark and just sooo many -all branches are infested and they have so many matured apples, persimmons, pears. They called for help but none knew what to do. They ended up cutting all the branches drastically so they were reachable and scraped off the trunks and discarded everything in the dumps.

Volk Oil (although I understand that any summer oil will do, like Sunspray, for instance) spray got rid of the scale on my lemon tree last year and once the scale was gone the ants went too. The ants 'herd' the scale for the honeydew but the main problem is the scale feeding off the tree.

Hi Lizzie,

Where do you buy Sunspray and Volk oil? Is it sold online? I'm hoping that I won't develop any bugs on my citrus, but nature always prevails and then you have to intervene.

GH

You can get Volk oil at any HD or Lowes...

I just noticed my Meiwa Kumquat is infested with dark brown scale insects. I have ants living under the bush so maybe they are farming them. The bush is just beginning to flower, I don't want to spray with anything that would hurt the flowers or bees. It looks like there are hundreds of the scale insects, how much alcohol are you supposed to use on a kumquat five feet high and five feet wide anyway? One 16 ounce bottle or a gallon or what? Will the alcohol hurt the plant?

You may want to just get rid of the ants and go get some ladybugs. The ants will protect the scale from beneficial insects, so they have to go first. Then if you reduce the population enough with the alcohol, the tree should be cleaned by the other good insects out there. Neem also seems to help, combined with some insecticidal soap.

As for alcohol I use it full strength with a brush or towel on the scale itself. Cant imagine it hurting the flowers as long as you dont distrub them yourself.