Many biological phenomena are inherently multiscale (MS) - i.e. they are characterised by interactions involving simultaneously different spatial and temporal scales. The needs of describing systems in a MS fashion and, more in general, MS problems across multiple scientific disciplines require a common modelling approach being able to (i) unify the common principles arising in general in MS scenarios (e.g. scale representation, scale separation and inter-scale interaction), (ii) support the effective combination of various single-scale models through well-defined scale coupling procedures, and consequently (iii) help to model and to simulate MS scenarios in a rigorous and systematic way. Complex Automata (CxA) constitute a well-defined paradigm for multiscale modelling that goes towards the above mentioned characteristics. BIOSHAPE, a 3D spatial geometric-based simulator, has been also defined as an independent modelling and simulation environment naturally able to represent, in the same model, different levels of multiscale systems. In this work we show that BIOSHAPE can be used to perform multiscale modelling and simulation using the same core ideas of the CxA approach.