Rock and metal nodes are the two mine resources. Rock nodes can produce stone which is used in many aspects one of which is in the city building area. Gems are used for crafting. Normal metal nodes can produce iron ore that can be smelted in iron ingots, while sulfur is a reagent that is applied to spell casting.
In order to mine any of these nodes, the tool you need is a pickaxe. To get the pickaxe works in the way: you walk up to the node, use R to unsheathe the pickaxe, and then aim at the node by left clicking.