Lignocellulosic biomass conversion to produce biofuels has received significant attention because of the quest for a replacement for fossil fuels. Among the various thermochemical and biochemical routes, fast pyrolysis followed by catalytic hydrotreating is considered to be a promising near-term opportunity. This paper reports on experimental methods used 1) at the National Renewable Energy Laboratory (NREL) for fast pyrolysis of lignocellulosic biomass to produce bio-oils in a fluidized-bed reactor and 2) at Pacific Northwest National Laboratory (PNNL) for catalytic hydrotreating of bio-oils in a two-stage, fixed-bed, continuous-flow catalytic reactor. The configurations of the reactor systems, the operating procedures, and the processing and analysis of feedstocks, bio-oils, and biofuels are described in detail in this paper. We also demonstrate hot-vapor filtration during fast pyrolysis to remove fine char particles and inorganic contaminants from bio-oil. Representative results showed successful conversion of biomass feedstocks to fuel-range hydrocarbon biofuels and, specifically, the effect of hot-vapor filtration on bio-oil production and upgrading. The protocols provided in this report could help to generate rigorous and reliable data for biomass pyrolysis and bio-oil hydrotreating research.