Hello everyone
I used a cylinder to bool-difference on a complex surface.
As you can see, the edge of the boolean is having normal-issues and is not bevel-able.
I am looking for a general workflow that allows me to create “good edges” without taking 1h+ to fix every vertex on its own.
You can use Weld modifiers to clean up close or overlapping Vertexes, but they are not clean.
Or you can use a remesh…
All automation methods are flawed, and I think the way to organize them perfectly is by hand. 
Select a circle to clean and X > Limited Dissolve. Drag the slider up to around 12 Deg. It will remove most of the unwanted (cylinder in your example) points.
It helps to keep an un-booleaned copy of the mesh so you can shrinkwrap the cut version onto the original - to fix the points on the cut edge that moved in / out.
The bevel will only work as far as the two points nearest each other. Which is about zero in your mesh.
Did you try selecting the cylinder section and doing an inset or an extrude? That may not work for this complex example… Obviously you should have joined the eyes too the rest of the head first.
Well… booleand are “famous” for not being suite to some forms especially with lots of edges and the solution is called apropriate modelling… no… no joking… it’s somekind of holy grail in polygon modeling… see for example on this very long living forum and thread:
