Fluxes and gemstones are purely there for you to sell using "/mine shop".
Artifacts come with a rarity level, I-IX (1-9), which is the main influence on how good the rewards will be from opening them. When you get an artifact it will be sealed, and while sealed it's stackable (and sellable to us).
To use them you need to take the sealed artifact in your hand and right-click to get an unsealed artifact, which are non-stackable. Be aware that if your inventory is full while doing this, the artifact will disappear! The unsealed artifact will display what loot you can get and at what chances.
To get the loot you need to open "/mine artifacts", put your unsealed artifact there and then wait the designated amount of time.
1. The unique loot from artifacts are fossils. Any rarity of artifact can drop a fossil, but the higher the rarity, the higher the chance. Fossils have no use apart from making them into a vessel, which give you various bonuses to the pickaxe you put it on.
2. To make a vessel you need to have all the 8 different fossils of the same name, put them in a refinery and press the fence. Put the vessel on your pickaxe and then open /mine vessels and click your pickaxe, and add a requiem to each of the empty spots beneath the iron bars.
3. You then need to play a "minigame" to find out which 3 requiems out of the 12 that exist are the right ones. The "minigame" is that every ore has a chance to spawn a thrall that increases your progress towards finding out what the next Requium is, or a boss which will tell you which your first wrong requiem is.
4. Once either one has spawned there's a two-minute cooldown until you can spawn a new one.
5. The order of requiums is random for each player, so you cannot ask someone else for the combination.
6. Once you've got all the three requiums in the right order, you need to kill the boss and then your vessel will be added to your pickaxe.