The problem of design optimisation of thin film direct current Superconducting QUantum Interference Device (SQUID) magnetometers made of YBCO (YBa2Cu3O7-x) was considered. The inductances and effective areas were calculated using the software package 3D-MLSI. Resolution and reliability issues were first tested on simple superconducting systems, showing good agreement with analytical formulae and experimental results, and demonstrating that a remarkable precision can be obtained though at the expense of CPU time and memory. The software was then used to simulate a SQUID magnetometer fabricated in the Device Materials Group of the Department of Materials Science and Metallurgy, proving that 3D-MLSI can be used to predict the parameters of real systems with acceptable accuracy.