Soul Motes can be harvested from Soulsprouts and Soulwyrms and mined from Soulspires. You need harvesting levels of 0 and 30 to harvest Soulwyrms and Soulsprouts, respectively. For Soulspires, you need a mining level of 50.
Soulsprouts can be found in large numbers throughout the low-level areas of First Light, Everfall, Monarch's Bluff, and Windward, but there are a couple of spots that reliably have large numbers. The first is the area around the Shattered Obelisk in Everfall.
The next is Light's Crown in First Light.
Soulspires a less common than Soulsprouts, but there are still some areas that provide nice farming opportunities. The first spots are in Mourningdale, to the north and east of the village. It's recommended that you are at least level 45 to travel through this territory safely.
The next two areas with lots of Soulspires are in southern Great Cleave. You'll need to be level 41 to handle this area.
Soulwyrms are much rarer than the Soulsprouts or Soulspires. You'll really only ever find one at a time when you stumble across one. It's not recommended to go hunting for them, but if you happen across one, be sure to grab it. You can harvest Soulwyrms at any skill level.
If you need Soul Motes, head to the places described above, and you should be able to get all the motes you need. Be sure to save your motes because they'll be essential to crafting high-level arcana items like tuning orbs, which allow entry to the expedition group content. if you happen across one, be sure to grab it. You can harvest Soulwyrms at any skill level.