Scanning tunneling microscopy (STM) images have been collected for a series of substituted alkanes and alkanols that form ordered overlayers at room temperature on highly ordered pyrolytic graphite surfaces. Molecules that have been imaged possess an internal bromide, with or without terminal alcohol groups (HO(CH2)(9)CHBr(CH2)(10)OH and H3C(CH2)(16)CHBr(CH2)(16)CH3), an internal -OH group (H3C(CH2)(16)CHOH(CH2)(16)CH3), and an internal methyl group (H3C(CH2)(16)CHCH3(CH2)(16)CH3). These data allow comparison to the STM image contrast reported previously for molecules in which -OH, -Br, and -CH3 groups were located in terminal positions of alkane chains adsorbed onto graphite surfaces. When the functional groups were in gauche positions relative to the alkyl chain, and thus produced molecular features that protruded toward the tip, the functional groups were observed to produce bright regions in a constant current STM image, regardless of the STM contrast behavior observed for these same functional groups when they were in terminal positions of adsorbed alkyl chains. These observations are in excellent agreement with theoretical predictions of the STM behavior of such systems. Additionally, several interesting packing structures have been observed that have yielded insight into the intermolecular forces that control the packing displayed by these overlayers.