Aim of this paper is to present an engineering tool for the design and modeling of the upgrading of three biomass derived liquids (bio-oil, vegetable oil and algal oil) through hydrotreating process for the production of advanced biofuels. For each case, the appropriate approach was followed regarding the model compound selection for each bio-feedstock, the main reactor modeling, the products separation and purification and the make-up hydrogen production. Simulation runs were performed in ASPEN Plus (TM) and revealed the importance for make-up H-2 production from recovered light gases and external fuel such as natural gas (the heat content on LHV basis if the inlet natural gas is 7.4% of the produced fuel in the jatropha oil case), showing also the beneficial impact of a good catalyst. The energy"balance calculations showed that the most energy demanding components are the air compressor before reformer and make-up H-2 compressor at the hydrogen production plant. The assumption of a chemical equilibrium can be regarded as a well-fitting and valid approach for the process design. The representation of bio-liquid by a model compound (Le. palmitic acid in case of algal oil) may result in good estimations in terms of mass (0.845 Kg(G-Diesael)/Kg(algal.oil) product yield) and heat balance of the total process (94.9% thermal efficiency) but all the detected fatty acid is suggested be taken into account for a more detailed analysis.