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I generally use a mix of fusion and meshmixer. Sometimes simplifying the meshes in meshmixer before importing to fusion makes your life a lot easier. Sometimes though it’s just easier and faster to model everything from scratch.
I think prusaslicer has also been adding some more tools for quick, simple edits also.
Editing stl files on fusion is tricky. If I can, I use tinker CAD. If I can't, I'll redesign the part to be parametric.
Meshmixer is good for exactly that but it's been a long time since I've used the software.
I've been very impressed with Prusa Slicers ability to do this kind of thing. I keep telling myself I'll do it in Tinkercad if I have any issues with Prusa slicer, but I always seem to accomplish what I need there.
I use tinkercad to do most things, especially when it comes to combining models, adding some shapes or holes, etc. It's easy to use, you aren't inundated with features you don't need, and always exports an STL that your slicer can understand. I use blender for more complex things, but I know like 2% of what blender can do, so it's easy to get lost in there.
I had some luck with this yesterday.
Attempt #1 was editing in blender, and it took 3h to get the file to slice correctly (I needed to remesh in blender sculpting tools to get the overlapping shapes to work).
Attempt #2 was importing the STL in openscad and doing a union() of the two objects. That worked perfectly the first time and took 20min. (But it was way more annoying to pick exactly the right number to translate all the shapes around)
I haven't found a good way to deal with that except sort of merging the stuff together and hope everything works out.
That's the main reason why I always publish my stuff in stl and step format
I use OpenSCAD for my prints. So it's just importing the STL with one line of code, and adding of substracting volumes.
I wish the 3D printing community would at least start uploading STEP files with their STL so people can edit without much trouble. So annoying to get something that has a license that allows editing but you are stuck with the garbage low resolution model that someone has exported that can't be edited directly.
Especially now that Prusa Slicer takes in STEP models I don't see a reason to use STL.