It's very do-able, as long as you know what you're doing and have the patience to do it. I start with taking apart the container that is holding the clone (cup, small planter, ect.) and maintain the root mass in one hand and sift the loose soil out of the roots. After you have the majority of the soil gone start getting your net pot/hydroton ready by lining the bottom, have a glass of PH'd water (I add my rooting nutrient as well only 1-2ml) and I dip the roots into the cup and allow the rest of the dirt to rinse off the roots, transplant directly into hydroton and put them under the lights. I have lost a few plants, but that's a risk of transplanting, knock on wood I haven't lost a transplant in about 6 months.
Give it a try if you still think its doable, but keep in mind the clones I would transplant were only 2-3 weeks from cut, with 2-4'' root beards so the development of your clones will determine how easy or difficult this process will be for you.