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Advancements in electronic integrated chip technology are slowing down with transistor sizes approaching their theoretical limit in most equipment and devices. As the data transmission rate has benefited from the telecommunication technology through optical fibers, Photonic Integrated Chips (PICs) are expected to fill the gap in the demand for higher transmission rates and faster computational speeds that the electronic chips would fail to fulfill. The research into PICs is in the center of attention in the academic and industrial fields, and the way in front of PICs development and improvement is still long. There are many opportunities including the use of new materials, different designs and architectures, and the use of various physical effects on the macro and micro scales. The main aim of this work is to design a hybrid-multi-layer PIC that allows the integration between an ultra-high-Q micro-resonator made of silica and an optical waveguide of a different material through a MEMS actuated coupler. To date, the ultra-high-Q silica micro-resonators can confine light within for the longest period, which is very beneficial for many applications including revolutionary accurate time measurements, and studying non-linear optical phenomena using modest laser powers. As using silica micro-resonators offers the highest-Q factor, using an optical waveguide of different material can offer the best operation condition based on the required application. For instance, having a silicon waveguide with high refractive index allows the fabrication of dense photonic chips, while using nanocrystalline diamond (NCD) waveguide suits wide-transmission-window applications. To achieve this goal, several studies were required along the way. For example, the hybrid-chip would include a suspended NCD waveguide structure that has not been demonstrated before. So we took the initiative and designed, fabricated and studied its operation. During fabricating the chips in this work, the ablation of NCD films using CO2 laser was observed, which was unexpected. As explanations in the literature was unsatisfactory, we hypothesized a new explanation, and confirmed it using numerical and experimental tests. After designing the hybrid-multi-layer PIC, we took the study a step further and developed the fabrication process. Also, an analytical formula for estimating the scattering loss from asymmetric rough rectangular waveguide surfaces has been formulated to assess the practicality of using specific waveguide designs using certain fabrication techniques. Finally, the design of grating couplers is presented as a starting point for prospective work. The work presented here is believed to be a beneficial milestone in the realisation of practical hybrid multi-layer PICs.