Internal error in boolean (A-B,B)

I am doing my major project where I have to do static analysis on the knee joint. I imported the stl files and made them into solids then deleted the mesh. I have made the model such that the parts superimpose each other. I am trying to do the boolean operation (A-B,B) to make shared surfaces between them so that I can get a node-to-node connection for final meshing. But at some places, it starts processing then it gives the message- internal error. I read somewhere that using all internal faces options might solve this problem. But it is not available in (A-B, Can anyone please help me in the same.
Also if there is another way to make a node-to-node connection then I can apply the boolean in the modeling software blender, from where I have exported the stl file.
Regards,
Aadarsh