You can obtain gems by exploring rare Crypts or crafting them using rare flickering dust. The only way to get rare flickering dust is by disenchanting gems. Much like crafting materials, gems can be upgraded by combining them.
To access the gem processing interface, click the Forge icon on the lower menu panel.
Next, switch to the Workshop tab. You will see three options in the Gems section.
All of these menus work much like the combination menu, which we discussed before.

To be able to craft gems, you need to have researched the "Gem crafting" technology in the Blacksmithing branch of the Academy. The higher the level of the gem that you want to craft, the higher the level of the technology that needs to be researched.