The effect of both chain length and temperature on the reactivity of alkanethiolate self-assembled monolayers (SAMs) with atomic hydrogen was studied via direct imaging of the surface throughout the reaction. These images were obtained with a ultra-high vacuum scanning tunneling microscope (UHV-STM) with a thermal gas cracker allowing for in situ exposure to atomic hydrogen. For a series of alkanethiolate SAMs 8- to 11- carbon atoms long (8C-11C), it was found that small increases in chain length caused disproportionately large decreases in reactivity at room temperature. This reaction progression was described by an exponential function with two rates: a slow rate for hydrogen reacting with standing-up phase, which is dependent on chain length, and a fast rate for low-density phase reactions, which is the same for all samples. Additionally, with the ability of the STM to observe molecular-scale changes in surface morphology, chain-length dependent changes in the sample were seen. For the shorter chain 8C and 9C samples, there was a significant growth in the average etch pit area over the course of the reaction, while few changes were seen in the 10C and 11 C samples. For decanethiol, it was found that decreases in the temperature of the SAM during exposure to atomic hydrogen caused corresponding decreases in the rate of the reaction. Additionally, it was found that between 250 K and 270 K the alkanethiolate molecules became immobile on the surface. The reaction at 270 K appears to proceed via the same pathway as at room temperature, while during the reaction at 250 K the surface evolves in a new manner. The same two-rate model was applied to the temperature-varied reactions. At 270 K and 290 K the model described the reactivity relatively well, suggesting that lowering the amount of thermal energy available in the SAM by lowering the is energetically equivalent to raising the intermolecular forces by increasing the chain length. When applied to the 250 K experiment, the model seems to describe the initial reactivity, when the slow rate dominates, but poorly describes the later, faster parts of the reaction, probably due to the lack of alkanethiolate mobility.