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Couldn't figure out how or what to mine. Pretty sure I ran into coal several times, but hitting it with the laser just turned it into a physics object instead of getting it.

On the surface there is a green box, it has a list of upgrades and tells you the required materials. In order to pick up mined minerals you have to press Q or B if you're using a controller, and you'll switch to tractor beam which allows you to pick up stuff.