delete overlapped part of faces I have more than a thousand places where this happens in a single mesh object. As you can see in the image, part of the faces are overlapping. I want to delete the overlapped part of the faces.    
Boolean modifier won't work because it's a single mesh that has many places where this happens.    
Remesh modifier won't work because it creates big blobs of new mesh were there doesn't exist anything.     
Blender doesn't recognize that as an "interior face" too so the seletect "interior faces" and delete method won't work either. How do I delete the overlapped part of the faces?
AFAIK there is no one-klick method for this and every possible way to pull this off requires a decent amount of work. Let's break down what we actually can do with the limited information about your model/scene you provide. 

Let's assume (by the look of the screenshots) that your model is a minecraft-like structure where the original blocks (before joining) only touch each other's faces and never intersect and they also don't have merged vertices. What we then can do with this, is separating the model into individual primitives quite easily. 

Tab into edit mode, hit A to select everything, then P to start separating and select "by loose parts" in the menu. 



Now, that we have separate blocks we could try combining the meshes step by step using the boolean modifier with the union operator. 

The bad news is that the boolean modifier might not work as expected on many occasions (if you have mesh intersections or the meshes simply have no connecting faces...) and with "more than a thousand" partly hidden faces this method will be so much work that you easily could reconstruct your model from scratch as well.