Hello,
from the 2 attached pics you can see I am trying to extrude manifold, But the sides are remaining?
Extrude Manifold isnt that powerful. Initially there was a much more powerful variant written by a contributor, but there was a discussion abouts the patches codequality and so they added this current version instead. And its much less advanced.
As you can see the same problem happens even in the demo in the manual, so no its simply an unsupported case.
https://docs.blender.org/manual/en/latest/modeling/meshes/tools/extrude_manifold.html
Thanks for the reply.
Have you tried this add-on?
its cheap enough, think i might buy it and see how it works.
The problem I had i just fixed manually with deleting faces and bridging. but it would be nice if this worked in the future.
No I havent tried that addon, but the developer is also regularly active here on this forum and from all I can say very helpful when questions and problems with their addons come up.
So theres no real risk in buying it if the featureset suits your needs.
i have a feeling its because there is slight tapers on the vertical edges.
I tried extruding manifold with normal orientation with the same result.
Thank you for the reply.
I did a test on a cube.
then i also read in the manual, that extrude manifold only dissolves orthogonal edges. google definition of orthogonal edges says aligned with axis, 90 or 270 degrees.
Extrude manifold and Extrude are basically thought to be the same.
I think the difference is that Extrude can only create face and Extrude manifold can also create face and delete face.
- Extrude cannot delete the detach face.
- Extrude manifold deletes the face.
- In this case, it is a modeling that goes down and then comes up again.
In this case, a Face is created inside the part of 3.
However, Extrude manifold does not create a Face for modeling like this.
As a result, Extrude manifold only works in the same way as Extrude, not in the form of modeling. 
this works 80-90% time and is really powerful. even can create holes while extruding. only few times it create manifold faces.
In the meantime, you can enable auto-merge and check split faces and edges, this way you can delete the unnecessary polygons that are created while extruding.
I ended up purchasing the punchit addon to see how it worked.
It works great!
Since both sides of my original mesh were tapered i would only be able to slide along one edge.
But that would have cut the auto-merge work in half.