its a physical process. seperating things based on specific gravity and size for the most part. i looked into this some time back after reflecting on how food mills operate.
some seeds are huge and heavy with respect to the fruit or cereal crop that is harvested. these can be mechanically broken away and isolated with vibration tables and sieves.
for small seeds... seeds that may not be terribly heavy or terribly light with respect to the fruit matter can be classified with jets of air in some cases, with vortex seperators(ever see a wood shop dust collection system?).
one of the main things with seed preparation is the drying of the seed... if i had to guess, the drying is done prior to any major classification. once the seed and accompanying fruit matter is dried out, i imagine classification via vibration or air, subsequent washing/fluidizing or seed treatment steps are after the seeds are dried.
by classification im referring to the grouping of materials by some physical means,according to weight, size or specific gravity.
imagine taking a bucket filled with cotton balls and lead shot... throw the contents of the bucket out as far as you can. you will find that the lead shot will travel further given that its less effected by drag compared to the cotton balls.
if you collect only the top 60% of the farthest flung material and repeat this task 10 times, with the same force, you will find that you have a substantially pure fraction of lead shot.
this is how aggregate is classified for concrete mixes and this is how gold is panned away form worthless sediment.
with very homogeneous mixes of junk, you can do very very fine classification with 'particle exclusion', meaning filtration. you start with a stack of sieves, with the largest ones on the top and the finest smallest mesh sizes on the bottom.
you shake the shit out of this stack of sieves for 20 minutes, and you will find that in every sieve you have some amount of very very homogenous, pieces that are virtually identical.
this is done with shit like soil samples mostly. its labor intensive and not terribly efficient.
notice the very agressive control of dust.
https://www.youtube.com/watch?v=TfiT-KKly0c