In the frame of the project MORA (Matter’s Origin from the Radio Activity of trapped and oriented ions), a transparent axially symmetric radio-frequency ion trap (moratrap) was designed in order to measure the triple correlation parameter D in nuclear $\beta $-decay of laser-polarised ions. The trap design was inspired from the lpctrap geometry, operated at GANIL from 2005 to 2013. In a real (non-ideal) Paul trap, the quadrupole electric potential is not perfect leading to instabilities in ion motion and therefore affecting the overall trapping efficiency. This paper presents a numerical method aiming to optimise the geometry of a trap. It is applied to moratrap in order to improve the trapping efficiency and to enlarge the axial transparent solid angle compared to lpctrap. In the whole optimisation process, numerical computation of electric potential and field was carried out using an electrostatic solver based on boundary element method (BEM). The optimisation consisted in minimising an objective function (fitness function) depending on higher order multipoles of the potential. Finally, systematic changes of trap dimensions and electrode displacements were applied to investigate geometrical effects on the potential quality.