Your skills level up as you use them. When you get a skill to a certain level, you can choose a perk from that tree. The perks available are based on your level within that skill. Perks you can assign appear light blue. Perks you need to level up more for appear purple. Perks you already have appear yellow. Here's a picture from a Skyrim wiki showing a perk tree with a mix of unavailable, available and assigned: As far as actually assigning the perks, you need to make sure you have perk points available (which you get when you level up), then click on a light blue perk, at which point you will be asked if you want to apply the perk point. You navigte through them with WSAD (or whatever keys you use to move) and assign them with Mouse1, or, if you're using a controller, navigate through them with the left stick and assign them with the button that attacks.