A systematic scanning tunneling microscopy (STM) study of alkanethiol self-assembled monolayers (SAMs) is presented as a function of the bias voltage, tunneling current, and tip-termini separation. Stable and etchpit free SAMs of close-packed undecanethiol/Au(111) were obtained after annealing in ultrahigh vacuum. STM revealed two distinct c(4 x 2) structures with four nonequivalent molecules per unit cell. For both structures, reversible contrast variations occur upon systematically tuning the bias voltage, the current, and the tip-termini distance. These contrast transitions originate from probing the corresponding local density of states (LDOS) of each molecule and not from the reorientation of the alkanethiol chains. The STM contrast is particularly sensitive to the tip-termini separation in the range of 0.5-2.5 angstrom, reflecting the distance-dependence of LDOS. At a fixed tip elevation, the STM contrast is less sensitive to changes in bias within 0.1-1.2 V. For the first time, we demonstrate that LDOS may override the physical height variations in the STM topographic contrast for alkanethiol SAM systems.