I don’t feel qualified to answer (but since when does that stop me?). I was using sketchup, with the stl plugin. I don’t like that it’s only windows, which requires a virtual machine, and sometimes, it decides a connected set of lines is a plane, and sometimes it doesn’t and I haven’t figured out how to fix that. Other than that, it works OK. If I was trying to do something complicated (other than just stretch a part or two), I would probably just import the stl, make it a component, and then redraw it, using the sketchup shapes, with the points of the stl as a guide. I think there are some neat pieces of software for just doing things like cutting along a plane, moving objects, and joining them (tinkercad, is that useful for that?) But if you want to do something more difficult, I think you’re basically stuck with recreating the part from the stl.
Ryan told me about onshape, and I’ve been using that successfully with stls as well, it’s easy enough to import an stl into a design, and then use it to make references for a “sketch” and then extrude what I need, or just save the sketch as a dxf, which is what I did for me MP3DP base.
I’m not a CAD expert, so maybe that’s useful to you. It’s annoying, because you have some small problem you want to solve, and immediately, you get a bigger problem plopped in your lap, which is how to learn to use some CAD software, and before that even, what CAD software to use…