Quantum opto-mechanics is a fast moving, broad research field which aims to investigate and control the interaction of light and the quantized motion of mechanical objects and the coupling between them. This allows one to engineer the mechanical quantum state by controlling and measuring the electromagnetic field, and conversely, to control the dynamical evolution of the optical field via its interaction with a mechanical system. Mechanical resonators are accessible in many different shapes and sizes, from kilogram scales in experiments that test gravitational theories to micro-and nano-scales in resolved sideband regime, where the frequency of the mechanical resonator is larger than the bandwidth of the optical cavity. In this regime, it is possible to cool the mechanical object to the ground state which allows a high degree of control and the ability to prepare interesting non-classical states, states that could aid in investigating the quantum dynamics of macroscopic objects. The field of quantum opto-mechanics is a promising testbed for quantum control technologies, such as fundamental tests of quantum mechanics, ultra-sensitive quantum sensors for precise measurements, phonon lasing, mechanical memories with long lifetime and quantum information processing. Furthermore, experiments are progressing toward strong opto-mechanical coupling regimes with single photons. This creates a platform that can take advantage of the nonlinear optical interactions to generate highly non-classical states in such light-matter interfaces. Photonic systems working in the single photon regime will be promising for low power applications and also for implementations of quantum information and computation.Motivated by these applications, this thesis consists of theoretical studies in the context of single photonics. This includes investigating non-classical mechanical state generation and mechanically controlling the dynamical evolution of optical fields in the strong coupling regime single photon opto-mechanics and furthermore, proposing a quantum sensor using single photonics. In this regard, we employ three important formalisms to treat and measure open quantum systems with non-Gaussian input fields: the conditional and unconditional cascaded master equations, Fock-state master equations and input-output Langevin equations. In the context of opto-mechanics, the system to be investigated is composed of two optical cavities with a coupling modulated via a mechanical resonator.In one case, a sequence of single photons are irreversibly sent to one of the optical cavities. After photons go through the opto-mechanical interaction, photon counting measurements are performed on the cavity output, conditionally steering the mechanical state to a highly nonclassical Fock state. Numerical calculations are performed to predict the experimental parameters needed to generate a mechanical Fock state before the mechanical object is thermalized.In another case, the same opto-mechanical scheme is employed to conversely modify the state ...