Quantum engineering using photonic structures offers new capabilities for atom-photon interactions for quantum optics and atomic physics, which could eventually lead to integrated quantum devices. Despite the rapid progress in the variety of structures, coherent manipulation of the quantum states of single atoms with photonic modes at the single quanta level has yet to be demonstrated. Here, we use the waveguide mode of a hollow-core photonic crystal fibre to manipulate the mechanical Fock states of single atoms in a harmonic potential inside the fibre. We create a large array of Schrödinger cat states, a quintessential feature of quantum physics and a key element in quantum information processing and metrology, of approximately 15000 atoms along the fibre by entangling the electronic states with the coherent harmonic oscillator states of single atoms. Our results demonstrate the first coherent quantum control of the atoms with the photonic structure and provide an essential step for quantum information and simulation with a wide range of photonic waveguide systems.