The pharmaceutical industry is currently dominated by the traditionally implemented, yet wasteful and inefficient, batch production paradigm. Continuous Pharmaceutical Manufacturing (CPM) shows potential to bring technological innovation, cost savings and environmental benefits to pharmaceutical firms. This paper describes the process modelling and simulation of CPM of two active pharmaceutical ingredient (API) cases: diphenhydramine (a globally-marketed antishistamine) and artemisinin (an important antimalarial drug), with focus on implementing a continuous separation process for each. The continuous liquid-liquid extraction of diphenhydramine and crystallisation of artemisinin are compared to the batch methods, in order to demonstrate the benefits of material efficiency and economic viability of continuous separations in pharmaceutical manufacturing.