_We have conducted an investigation of the interaction of a series of n-alkanes with the surface of highly ordered pyrolytic graphite (HOPG) using scanning tunneling microscopy (STM) and molecular dynamics (MD) computer simulation. The alkanes studied in this work (CnH2n+2with n=16, 17, 20, 28, and 32) yield STM images which are highly suggestive of an ordered quasi-two-dimensional phase on the graphite surface. Individual molecules on the graphite surface adopt a rod-like conformation and are arranged in a 'rank-and-file' structure. Analysis of the STM height profiles indicates the presence of two dominant spatial frequency components. The high-frequency component has a period of about 0.30 nm and is independent of the carbon number of the alkane. The low frequency components have periods ranging from 3 nm to 5.5 nm. These values correlate closely with those obtained from estimates of the length of fully extended alkanes and from molecular dynamics computer simulations of surface-adsorbed alkanes. These direct experimental observations of surface ordering and the associated molecular dynamics simulations provide key new insights in elucidating the mechanisms of molecular adsorption on surfaces and thin films. In addition, the data helped resolve two conflicting mechanisms of alkane adsorption which have appeared in the recent literature.