Manipulation and transport of objects using mobile robotic platforms is a well studied field with several successful approaches. The main difficulty while using such platforms is the lack of adaptation capabilities to changes in the environment and the restriction to flat working areas. In this paper, we present a novel manipulation and transport framework using the self-reconfigurable modular robots Roombots to collaboratively carry arbitrarily shaped passive elements in a non-regular 3D environment equipped with passive connectors. A hierarchical planner based on the notion of virtual kinematic chain is used to generate collision-free and hardware-friendly paths as well as sequences of collaborative manipulations. To the best of our knowledge, this is the first example of manipulation of fully passive elements in an arbitrary 3D environment using mobile self-reconfigurable robots. The simulated results show that the planner is robust to arbitrary complex environments with randomly distributed connectors. In addition to simulation results, a proof of concept of the manipulation of one passive element with two real Roombots meta-modules is described.