This paper focuses on the atomic indentation and friction properties of self-assembled monolayers (SAMs) by a novel hybrid molecular simulation approach. By introducing a sliding dynamics for the tip-cantilever assembly in atomic force microscopy (AFM) and a fast molecular dynamics relaxation algorithm for SAMs, we simulate the scanning process of the assembly over SAMs in the time scale of AFM experiments. For the atomic indentation of SAM surfaces, we find that elastic modulus is chain-length independent, and has a value of 20 +/-10 GPa. However, under shear, effective shear modulus is found to be chain-length dependent, which explains the SAM chain-length dependence of friction observed in AFM experiments. The calculated surface energy of methyl terminated SAMs is consistent with many experimental results.