I did the same thing (build my mob spawner in a magical forest) I cleared it out by making a warp page to the top of the mob spawner. I then went far enough away from the mob spawner so that they would despawn and warped to the top. It was empty! To deal with the wisps I used conveyors to push the mobs into invar spikes and used a vacuum hopper to collect the drops. The mobs did not travel vertically. My drop shaft is unused. But hey the mob spawner is clog free now!I set up my mob drop trap in a magical biomes to try and spawn pechs. I was trying to figure out why I was getting so few mobs in my drop trap after a while. I changed the zoom and saw on my map radar, that the entire spawn area was filled with wisps. Yea for essence, sucks for clearing. It's not fun trying to clear out a 19x19 dark room full of wisps.
Don't make your mob drop trap in a magical forest biome. Sure you get pechs, but you also get wisps, and wisps fly and thus aren't subjected to the conveyor belts and subsequent drop.
I placed a grinder in one of the walls, and got about 1/2 a stack of essence in just a couple minutes. That's only 1 small section, and the grinder can only reach a 5x5 area.
I'm going through the process of turning off the dark room by replacing blocks in the roof with glass, and trying not to get killed by wisp lightning along the way. Once the dark room is turned off, I figure a few grinders in the walls should take care of the wisps eventually.