Verified answer

Like said you can't make them you find them.

2 guaranteed gems are found in 2 different locations:

Inner Sanctum (Markarth) ■There is a Flawless Sapphire and a Flawless Amethyst in the Dibella Temple in Markarth. Inside the Inner Sanctum on a shelf.

Korvanjund Crypt (The Pale)

You can't make them flawless D:. As you level higher though, you start to find more flawless gems. Level 81, ran through a dungeon and cleared it, had 32 flawless gems on the way out. If you need a way to use them better for jewelry, get transmutation. It is found in Ansilvund Excavation NE of Riften. Buy Iron Ore at a shop, Use Transmutation. Look at inventory, you will have silver. Use it again, look, you will have smeltable gold ore! One Flawless Sapphire should throw you in about 1k per ore. Happy Hunting!! If under level 10, you will have trouble moving through Ansilvund. It is full of draugr and ice warlocks that can freeze you. I found a bone dragon the other day :3.

Skyrim Jewels

You have to find them you can't make them.