Q.Cleaning out perennials, lilies, ferns etc. in fall
Should I do this clean up and cutting back in fall or leave the dead stuff to protect the plant?

Certified GKH Gardening Expert
It's your choice. Some people leave the foliage to protect the plants from cold winters, however, then pests and disease can overwinter in the dead leaves. But, if you garden for butterflies, you want to leave the foliage in case you have overwintering butterfly eggs, pupae, or adults. I sometimes will cut things back, but put the stems in a corner of the yard in case there are chrysalises.
In the case of lilies, you should let the foliage die back before removing those leaves. That is how the bulb is regenerated, just like tulips and daffodils.
Some people don't like the untidy look and will cut everything back in fall. I wait till spring to do most cleanup because I have butterfly host plants.
https://www.gardeningknowhow.com/garden-how-to/info/cleaning-up-garden.htm