The ability to quickly fabricate small unmanned aircraft system (sUAS) through Additive Manufacturing (AM) methods opens a range of new possibilities for the design and optimisation of these vehicles. In this paper, we propose a design loop that makes use of surrogate modelling and AM to reduce the design and optimisation time of scientific sUAS. AM reduces the time and effort required to fabricate a complete aircraft, allowing for rapid design iterations and flight testing. Co-Kriging surrogate models allow data collected from test flights to correct Kriging models trained with numerically simulated data. The resulting model provides physically accurate and computationally cheap aircraft performance predictions. A global optimiser is used to search this model to find an optimal design for a bespoke aircraft. This paper presents the design loop and a case study which demonstrates its application.