Flexible molecular brushes have exhibited extraordinary conformational and phase behavior that is largely a result of their brush-like architecture. The interaction between the densely grafted side chains controls both the conformation of the flexible backbone (hence molecular shape) and the intramolecular interactions (hence ordering and mixing). The unusual behavior of molecular brushes was especially evident when studying either single adsorbed molecules or dense monolayers on substrates. Molecular imaging by atomic force microscopy in combination with Langmuir-Blodgett monolayer characterization and replication via a PFPE-based soft-lithography technique proved to be an invaluable tool to characterize molecular weight distributions, individual branch size distributions, and conformational transitions of individual brush-like macromolecules. These molecules were observed to undergo discrete conformational transitions in response to changes of substrate area and substrate chemical composition. The transitions depended on the details of the molecular branching architecture as well as the molecular chemical composition. In addition to the molecular properties, the brush architecture stabilized the ordering of disk-like macromolecules and enhanced the mixing of two otherwise immiscible polymers. Not only did they mix, but they also exhibited an ordered structure of alternating hydrophilic and hydrophobic molecules.