Evaporation of Cu metal onto thin (less than 5 nm) molecular layers bonded to conductive carbon substrates results in electronic junctions with an ensemble of molecules sandwiched between two conductors. The resulting devices have previously been characterized through analysis of current density-voltage (j-V) curves for several different molecular layers and as a function of layer thickness. The approach represents an 'ensemble' rather than 'single molecule' technique, in which the electronic response represents that of a large number of molecules (10(6)-10(12)) in parallel as well as the conducting contacts contained in the molecular junction. In this paper, we extend a more detailed investigation of two critical issues: the possibility of conduction by metal filaments, and the potential role of top contact oxidation contributing to the electronic properties of the junctions. The results show that the conductance of the junctions can be modulated by changes in the deposition environment, but that the changes are not related to Cu oxide in the top contact. Based on these results, we propose that the conditions during top contact deposition change the way in which the molecules contact the metal, leading to differences in the effective junction area. Finally, through systematic studies using variation of the temperature, we show that metal filament conduction is distinct from that observed for the molecular junctions and that if the current observed experimentally passed through nanoscopic metal filaments the Joule heating would lead to rapid melting. For a series of junctions with structurally related aromatic molecules (including biphenyl, nitrobiphenyl, fluorene, and nitroazobenzene), the electron transfer mechanism is briefly investigated using area-independent analysis methods. It is shown that field emission and/or transport through bands formed by the molecular layer is likely, based on the weak temperature dependence of junction conductance.