To advance commercialisation of ocean wave energy and for the technology to become competitive with other sources of renewable energy, the cost of wave energy harvesting should be significantly reduced. The Mediterranean Sea is a region with a relatively low wave energy potential, but due to the absence of extreme waves, can be considered at the initial stage of the prototype development as a proof of concept. In this study, we focus on the optimisation of a multi-mode wave energy converter inspired by the CETO system to be tested in the west of Sicily, Italy. We develop a computationally efficient spectral-domain model that fully captures the nonlinear dynamics of a wave energy converter (WEC). We consider two different objective functions for the purpose of optimising a WEC: (1) maximise the annual average power output (with no concern for WEC cost), and (2) minimise the levelised cost of energy (LCoE). We develop a new bi-level optimisation framework to simultaneously optimise the WEC geometry, tether angles and power take-off (PTO) parameters. In the upper-level of this bi-level process, all WEC parameters are optimised using a state-of-the-art self-adaptive differential evolution method as a global optimisation technique. At the lower-level, we apply a local downhill search method to optimise the geometry and tether angles settings in two independent steps. We evaluate and compare the performance of the new bi-level optimisation framework with seven well-known evolutionary and swarm optimisation methods using the same computational budget. The simulation results demonstrate that the bi-level method converges faster than other methods to a better configuration in terms of both absorbed power and the levelised cost of energy. The optimisation results confirm that if we focus on minimising the produced energy cost at the given location, the best-found WEC dimension is that of a small WEC with a radius of 5 m and height of 2 m.