In this paper, we introduce a simple global minimisation approach that is able to find minimum energy configurations of clusters containing aromatic molecules. The translational and rotational perturbations required in Monte Carlo-based methods often lead to unrealistic configurations within which two or more molecular rings intersect, causing many of the computational steps to be rejected and the optimisation process to be inefficient. Here we develop a modification of the basin-hopping global optimisation procedure tailored to tackle problems with intersecting molecular rings. Termed the Sphere Encapsulated Monte Carlo (SEMC) method, this method introduces sphere-based rearrangement and minimisation steps at each iteration and its performance is shown through the exploration of potential energy landscapes of polycyclic aromatic hydrocarbon (PAH) clusters, systems of interest in combustion and astrophysics research. The SEMC method provides clusters that are accurate to 5% mean difference of the minimum energy at a 10-fold speed up compared to previous work using advanced molecular dynamics simulations. Importantly, the SEMC method captures key structural characteristics and molecule size partitioning trends as measured by the molecular radial distances and coordination numbers. The advantages of the SEMC method are further highlighted in its application to previously unstudied heterogeneous PAH clusters.