Problems in creating a matching or perfect joining partner for a part with rough surface(Tetrahedral mesh)

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Hello,
I have a part with nodal coordinates and Element connectivity(Tetrahedral mesh). I want to create a part similar to the given part and they both should mate perfectly. So just reflection doesnot solve my problem. So what I did is I extracted the bottom surface of my input part which gives a surface with triangular mesh and is extruded in the downward direction and meshed it with tetrahedral mesh(iso2mesh tool box). But the number of elements on the initial surface before extrusion is changed in the way the number of nodes and elements are changing. Please tell me how to make it same.For me only the interface surfaces are needed to be same and other than that no problem.
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