Microalgae have great potential as a feedstock for the production of a wide range of end-products under the broad concept of biorefinery. In an earlier work, we proposed a superstructure based optimization model to find the optimal processing pathway for the production of biodiesel from microalgal biomass, and identified several challenges with the focus being on utilizing lipids extracted microalgal biomass for economic and environmentally friendly production of useful energy products. In this paper, we expand the previous optimization framework by considering the processing of microalgae residue previously treated as wastes. We develop an expanded biorefinery superstructure model, based on which a mixed integer nonlinear programming (MINLP) model is proposed to determine the optimal/promising biorefinery configurations with different choices of objective functions. The MINLP model is solved in GAMS using a database built in Excel. Economic sensitivity analysis is performed to elaborate the potential improvements in the overall economics, and set the targets that must be achieved in the future in order for microalgal biofuels to become economically viable.