After joining both the mesh i want to sculpt it so that i dont get a edge line between both the mesh where its join. Any suggestion how it works. Thanks join mesh.blend (2.4 MB)
First in Boolean modifier try decreasing Ovelap threshold to a very small amount.
When that wont help try enabling 3DPrint addon (comes natively with Blender) - it has some tools for mesh analysis, so you can find the problems like non-manifold geometry that might creating your problem.
In edit mode this addon lets you highlight the parts of the mesh with particular topology errors.
You can try increasing the extrusion where the two meshes overlap each other. I have had this problem before I needed to increase the overlapped areas. Any *air in it could mess up the boolean operation.
The effect you have after it’s because you probably have non-manifold geometry inside your mesh. That is a byproduct of applying boolean modifier to a mesh with bad topology or bad normals as @humanartist said. Try analyzing the mesh first.