This paper presents the development of a computer-aided decision support tool for identifying optimal biorefinery concepts for production of biofuels at an early design stage. To this end, a framework that uses a superstructure-based process synthesis approach integrated with uncertainty analysis is used. We demonstrate the application of the tool for generating optimal biorefinery concepts for a lignocellulosic biorefinery. In particular, we highlight the management of various sources of data, the superstructure (integrated thermochemical and biochemical conversion routes) needed to represent the design space, generic but simple models describing the processing tasks, and the formulation and solution of an MINLP problem under deterministic and stochastic conditions to identify the optimal processing route for multiple raw materials and products. Furthermore, we evaluate the impact of market price uncertainties on the optimal solutions and calculate the associated risk to enable informed and risk-aware decisions.