Although design optimisation has been well explored using mesh-based approaches, little work has been performed with meshless simulation. Equally, design optimisation has been well explored for methods capable of representing a single design topology, but much less well explored are methods that allow for optimisation of design geometry and topology. To allow for topology changes in design, a new volume-based parameterisation method is proposed which uses the fraction of volume that is solid in an underlying parameterisation grid as the design variables. This technique can be easily used with a low number of design variables, making it usable with agent based global optimisation methods and black box solvers. Optimisation of a NACA 0012 aerofoil in transonic flow is performed with the new parameterisation method and multi-body aerofoil configurations are obtained for optimisation with supersonic flow. Optimising the design of a pivoting, fluid filled tank, shows that the damping of the tank motions can be affected by the tank geometry, which suggests that the wing fuel tanks can be designed to alleviate the flutter instability. It is shown that the effect of fuel is to raise the flutter boundary so the concept of optimising tank design is explored by optimisation of the external tank geometry and by optimising interior baffle configuration. Orifices for vascular self healing networks in composites are optimised to increase mass flow rate. Additionally, the flow of self healing resin into a representative composite crack geometry is modelled using a smoothed particle hydrodynamics solver which incorporates surface tension. The design of a coastal defence structure is also automated through an optimisation process with the fluid behaviour being modelled by smoothed particle hydrodynamics. These optimisation cases have produced novel designs but also, importantly, demonstrate the versatility of the volume based shape parameterisation and the importance of topological change in fluids optimisation.