I ideally would prefer to have three independent objects and merge/join all 3 objects as one and export as an stl. I am aware of the 'join' function but this would not eliminate the overlapped boundaries in the stl file (that is the stl file still marks the boundaries of the objects present in the joined stl) which is not what I want. Therefore, I taught 'difference' boolean can be used but was causing major issues.
Now, I extrude each object individually and select a plane to apply the difference boolean. Unfortunately, this works very rarely and most of the time I end up with an unsnapped plane as in Fig.5. How can I avoid this?
For reference, I attach the blender file with 3 objects. I have not included the extrusion of the objects and difference boolean in the .blend file to make it flexible to work for others.
Do note that, I am using a maximum number of vertices for the math function (1024) as for my purpose I would like to have accurate tangents and normals to the surface. I did try out the "remove double" but still, I have some unwanted parts in the geometry.