When growing bonsai from scratch, and I mean, really scratch, so from seed, you are confronted with a thing called taproots. During the first stages of germination, many plant species grow a strong root straight down into the ground. This root provides initial stability to the sapling, and provides access to deeper laying ground water, required for sustained growth even in times of drought. As a bonsai, this taproot is not needed. So, after growing the tree for one or two years (Depending on the species, a plant may have a pencil-thick main stem within one year. If the tree is no at least 0,5 cm thick after the first year, wait another year before trimming the main root, to ensure the plant has enough energy to quickly recover) this taproot may be removed. A number of methods exist. Personally, I only have experience with the blunt method of just cutting off the taproot.
Cut off the taproot
Once the plant is thick enough the tree is ready to have the taproot trimmed. Dig up the plant, and trim all of the root away, leaving only a few cms of the taproot. Typically, this section will have a number of thin roots on the surface. Be carefull not to damage these.
Before replanting the sapling, insert a root-barrier in the planting hole. This can be anything from a piece of plastic to a tile or piece of wood. The only job it has is to stop roots growing down, and force them side-ways. Do this when the plant is going into dormancy. When the foliage of the tree has started to turn colour, the plant will still move nutriens around for several weeks. Cutting the taproot now will allow some of the nutrients to be stored in new roots. Or you could wait untill the plant is fully dormant. Plant the sapling deeper than it was, to ensure the rootstum does not dry out and is protected agains the first frosts. Protect against drying out. After another growing season dig up the plant again, and clean out the new roots as you would for any nebari.
Ground layer the main root
By moving the sapling into small holes drilled in e.g. a ceramic plate, or by slipping the sampling trough the centre-hole of the CD you create a tourniquette. This will interrupt the flow of nutrients and stimulate the forming of surface roots. After one or two years of growth, enough roots should have formed to sustain the plant. Trim the root below the disk and replant as normal.