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Minerals would be placed in patches of great density underground. Searching for them would be performed using stationary drilling machines. They would be placed somewhere (yes somewhere) and tell what is underground, the density of minerals in each chunk and what type of mineral. (Maybe even underground oil?) Finding a good patch of minerals would require a lot of drilling and it will be both resource and time consuming. Drilling machine could be relocated somewhere else after completing geological survey (the minerals aren't going to move, are they?).

This gives a good reason for satellite - orbital x-ray scanning would reveal minerals on whole map.

I see different methods to do this

>>Easy
Just place the mine above the patch and watch it mine. (There are mods for that now.) This can be enhanced that mine will take more time to mine chunks that are further from it.

>> Medium
Place the mine shaft above the patch and feed it with necessary equipment like drills and adit reinforcement (from wood or steel), transport belts etc.

>> Hard
Make another layer that player can enter and actually use machines that mine. Make minecraft but with machines and robots. Sounds fun right?
(And when there is a layer of terrain underground, maybe one up in the skies ?)
There are mods for that:
viewtopic.php?f=97&t=25444
viewtopic.php?f=97&t=19178

>> Mines could produce not only the minerals player wants but also a lot of rocks.
>> Mining could deplete current chunk and then move to next chunk, but with lower efficiency because it is further.