Furfurylation of wood is of interest worldwide as an environmentally friendly modification process. It is widely assumed that low-molecular weight furfuryl alcohol (FA) can penetrate into wood cells and polymerize in-situ during the process, resulting in substantial improvement in the physical-mechanical properties and durability of wood. In this study, confocal laser scanning microscopy (CLSM) was used to visualize the microscopic distribution of polymerized FA resin in the Masson pine wood cavities, and a Nanoindenter was used to probe the mechanical properties of modified wood cells. The effects of catalysts (maleic anhydride and a mixed organic acid catalyst), FA concentration, curing time, and curing temperature on the nanomechanical properties of wood cell walls were investigated. An improvement in the indentation modulus and hardness of modified wood cells demonstrated indirectly but strongly that FA indeed penetrated wood cells during the modification process. Based on the results of the cell wall nanoindentation test, a combination of 50% furfuryl alcohol, 8 h curing time, and 95 °C curing temperature were proposed as the starting processing parameters for the development of a more practical and effective wood furfurylation process using a mixed organic acid catalyst.