Molecular dynamics (MD) simulations were conducted in order to study the dynamic behavior and traction of bilayer lubricating films of n-hexane, cyclohexane, and n-hexadecane. Lubricants were confined between bcc iron surfaces with and without transverse grooves of mono-atomic depth. Once the system equilibrated statically, one of the solid surfaces was moved to shear the film. The results demonstrated that the traction coefficient was governed by structures of the films, which depended on the molecular structures of the lubricants and on the atomic scale geometry of the solid surfaces. Traction was high when interfacial slip between lubricant layers and solid walls occurred. Evolution of the layered structure by gradual rearrangement of the molecules and resulting slip between the lubricant layers, caused significant reduction in the traction coefficient. The atomic steps enhanced the molecular rearrangement of n-hexadecane, while they retarded or inhibited those of n-hexane and cyclohexane resulting in a relatively higher traction coefficient for stepped surfaces. Molecular orientation of the normal alkanes under shear is described by the orientational order parameter, which has a strong correlation with the traction coefficient. The steady state traction coefficient of all the three simple hydrocarbons was highest when both of the surfaces had steps, and lowest when both of the surfaces were flat.