I have a mesh with a lot of self intersections I got from running the shell modifier and I will later do some Booleans on it and then 3d print it. The trouble is the intersections throw off the Boolean modifier and make it give inconsistent results so these intersections must be removed before this step. Is there a way to remove these intersection automatically? Right now my workflow involves exporting the model to Meshmixer, running "make solid" and then importing the stl back into Blender. Is there a way to keep the workflow in Blender without adding hours of manual cleanup to remove hundreds of self intersections? If possible I'd like to keep the workflow entirely in Blender for scripting and license purposes in the end use case.
Remesh Modifier is Blenders equivalent of Make Solid in Meshmixer. But the results are unpredictable most of the time so I suggest you stick to Meshmixer for that operation.