Join overlapping objects/meshes into one surface in Blender I have a lot of spheres imported from the pdb-import plugin, which make up a molecule. I chose the radii of the spheres large enough, that all individual spheres overlap somewhere with others and this should form one closed object.

I cannot find a single tool to merge/weld/join/whatever the faces where they overlap to form just one uniform mesh surface without hidden faces on the "inside" of other objects.

The Mesh > Faces > Intersect and a simple Object > Join do not seem to do what I want to achieve.

For reference concerning the pdb-plugin, I have done Apply > Make Dupliverts Real and Object > Convert > Mesh as suggested.
I would use the boolean modifier to union them together.

Lets say I have 3 overlapping spheres i want to make into one, connected object.


Select one sphere, and create two boolean modifiers, both set to Union, with the other spheres as the objects:


Hit apply, and you can now delete the original two spheres. the third sphere with the boolean modifiers should now be one mesh that makes up all 3 spheres: