After Effect’s Fill effect is a very useful effect. If you have never used you probably should look into it. It’s the simplest effect. It just applies a color onto a layer. Basic stuff.

The weird thing with this effect is that its opacity property acts the same as with the Transform effect. It just bypasses the layer’s opacity. I’ve thought long and hard about why the After Effects team could’ve made that decision and never got to any conclusion. This feels like a bug that was called a feature but let’s give them the benefit of the doubt.

CC Composite is the solution

Now, there is a somewhat simple, yet not evident, way to fix this. The magic of CC Composite, a lesser-known effect that allows to composite your initial layer in your layer’s effects stack.

So, after you have applied your fill effect, don’t touch its opacity property and add the CC Composite on top of it and use the CC Composite‘s opacity property instead.

The only thing is, the opacity will feel inverted. CC Composite Opacity: 100% = Fill Opacity: 0%
If that really annoys you, create a Slider Effect and into the CC Composite‘s opacity property add the expression:

100 - effect("Slider Control")("Slider")

I would then advise you to save those effects as a Preset for reusability. If you use VideoCopilot’s FX Console (and you probably should), you can even alias this preset to the name “Fill”. That way you won’t have to deal with this weirdness again.

If you want to learn more about the CC Composite, Motion Array is a good reference: https://motionarray.com/tutorials/after-effects-tutorials/how-to/cc-composite-an-overlooked-effect.