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Sorry, but you're stuck with all those layers. I fear. After Effects is all about layers, and that's how it works.
Actually, it's a good thing it DOESN'T work the day you'd like.
In PP, you can apply an effect to just a single clip on a track, no problem. But in AE, you apply an effect to the entire layer. If this layer happened to contain several clips, only one of which needs the effect, you'd either suck it up and apply the effect to the whole layer, or you'd split the layer in a couple of places to isolate that one clip.... and the end result would be more layers.
PP and AE: they're two different applications for two different purposes, and they just don't work the same way.
3 people found this helpful
After Effects is for creating shots you cannot create in a NLE, not for editing or working on sequences. If you have 100 shots in your Premiere Pro sequence you'll have 100 layers in After Effects. If you have 100 shots and 10 audio tracks, you'll have 110 layers.
Tell us exactly what you are trying to do and we can give you some guidelines but your question tells me that you do not have a good understanding of how AE works or what it is used for. It is incredibly inefficient and time consuming to try and work on sequences in After Effects. It was never designed for that kind of workflow.