So far I found from creation kit wiki

Actors:
Lvl- "Leveled actors (Prefixed "Lvl") contain information telling the game what to spawn based on the players level. For example, LvlBanditMelee2H will spawn a Bandit with a 2-Handed weapon. You don't know if they will be male/female, or use a War Hammer, Battleaxe, or Great Sword. Those details are randomized."

Enc- "Encounter actors (prefixed "Enc") are non-randomized characters and creatures that typically populate Leveled Lists (EncBandit01Melee1HImperialF01/02/03/etc...). For example, if you need a Skeever you'd just simply place an EncSkeever actor. You always know that this placed reference will spawn a Skeever when you enter the level. This is also the way you'd place something like a EncFox, EncDeer, or EncSabreCat."

But I also see other prefix like "DUN" "CW" "MQ101" etc.

Can anybody explain what those mean?

They're also just handy references to what each thing is related to. Dunno about DUN and CW, but MQ101 probably refers to something related to stage 101 of the Main Quest.

If I had to guess Dun=Dungeon & CW= Civil War