Delete downfacing roots and radially arrange the remaining ones according to feasibility in the tree and your skillfulness in the practice.
If the material doesn’t lend itself to this, as
@Bonsai Nut says, move on to other material (or else suffer through wounding/moss-packing/hormoning and slowing down the material to try to ramify the roots, and accept the steep time cost vs better material. If seedlings are otherwise plentiful this can be a waste of time).
The younger a pine seedling is, the more likely you are able to intervene safely and with good results.
At 5 years, it’ll be tricky. At 5 weeks, you might be doing the taproot seedling cutting method and able to achieve a near perfect result (and should consider field growing pine prebonsai for a living, as this is step one).
I’ve collected my share of wild pine seedlings and IME this is a site-specific challenge. If the site is prone to drought or drainage (pines often compete for these sites) then you will discover a tap root since drought tolerance leans on early root colonization and sources may be deep.
If you do mess with restructuring collected seedling root systems “from scratch”, bottom heat (29C / 85F) is your secret magical superpower.