Microalgae's aquatic, non-edible, highly genetically modifiable nature and fast growth rate are considered ideal for biomass conversion to liquid fuels providing promise for future shortages in fossil fuels and for reducing greenhouse gas and pollutant emissions from combustion. We demonstrate adaptability of PRO/II software by simulating a microalgae photo-bio-reactor and thermolysis with fixed conversion isothermal reactors adding a heat exchanger for thermolysis. We model a cooling tower and gas floatation with zero-duty flash drums adding solids removal for floatation. Properties data are from PRO/II's thermodynamic data manager. Hydrotreating is analyzed within PRO/II's case study option, made subject to Jet B fuel constraints, and we determine an optimal 6.8% bioleum bypass ratio, 230°C hydrotreater temperature, and 20:1 bottoms to overhead distillation ratio. Process economic feasibility occurs if cheap CO2, H2O and nutrient resources are available, along with solar energy and energy from byproduct combustion, and hydrotreater H2 from product reforming.