While frictional behavior has been studied for millennia, trial-and-error approaches to materials selection for sliding systems remain prevalent due to a lack of understanding of the underlying mechanisms of friction. This thesis discusses uses of atomic force microscopy to probe the atomic-scale mechanisms that drive frictional behavior on two-dimensional and layered materials. By independently varying specific physical parameters, a more robust understanding of the intrinsic frictional behavior between materials can be developed. First, it is seen that increasing humidity initially increases friction by creating energetically favorable “pinning” sites on the substrate surface from the adsorption of water molecules. At higher humidities, the large water coverage eliminates the preferential points, thus decreasing friction again. Secondly, it is seen that adhesion will decrease logarithmically with increasing scanning speed. This phenomenon is attributed to a depletion of bonds across the tip/sample interface due to the faster sliding speed. Thirdly, sample deposition methods modify the frictional behavior of MoS2 monolayers, as the stronger adhesion between grown MoS2 and a silicon substrate reduces the monolayer’s ability to conform and create high contact quality compared to exfoliated MoS$_2$. Exfoliated MoS2 shows a friction contrast between monolayer and bilayer regions, while grown MoS2 shows no contrast. Fourthly, the friction force decreases as chalcogen size increases in MoX2 (X=S, Se, Te) such that the friction force follows MoS2>MoSe2>MoTe2. An increase in chalcogen size increases the lattice spacing, creating a wider pathway that allows the tip to detour around high energy sites and thus lower friction. Finally, the friction force on MoS2 shows two behaviors—a strong enhancement of friction at low temperatures or an athermal behavior, with this bifurcation attributed to a change in energy barrier to sliding due to tip changes or advantageous adsorbates. The thermal Prandtl-Tomlinson model does not fit well to the experimental data, highlighting the limitations of its underlying assumptions. Collectively, these results demonstrate the need to examine tip, sample, and substrate interactions and their role in atomic-scale stick-slip friction. The understanding of the nanoscale mechanisms influencing frictional behavior will help advance tribology research toward the goal of predictive, judicious, application-specific materials selection.