Scanning tunneling microscopy (STM) has been used to study the adsorption of 1-fluoro-, 1-chloro-, and 1-bromo-substituted C-12 alkanes at the Si(111)-7 x 7 surface, at temperatures from 300 to 500 K. We report self-assembly of these physisorbed adsorbates, C12H25X, to form approximately circular corrals, (C12H25X)(2), with charge transfer to a corralled adatom in each case (cf. Dobrin et al. Surf. Sci. 2006, 600, L43). The corrals comprised pairs of semicircular horizontal long-chain molecules stable to similar to 100 degrees C. At >= 150 degrees C the corrals desorbed or reacted locally to imprint a halogen atom, X-Si, and an adjacent alkane residue, R-Si. The corral height profiles, together with the location of the imprinted X-Si resulting from thermal or electroninduced surface reaction, led to a picture of the molecular configurations in these haloalkane corrals, (C12H25X)(2), X = F, Cl, Br, and the dichloro corrals, 1, 12-dichlorododecane, (ClC12H24Cl)(2).