Recent advances in the design and solution phase assembly of novel addressable DNA nanostructures motivate the development of new techniques for controlling deposition of the structures on surfaces. Both precise positioning of the nanostructures on patterned surfaces and purification of impure nanostructure product should be possible if structure-template interactions are properly tuned. Here we describe our efforts to characterize the interactions between DNA nanostructures and oligonucleotide functionalized gold films. Surface plasmon resonance (SPR) is used for real-time monitoring of the hybridization of DNA structures, such as four-arm junction tiles and superstructures such as fixed length track, on oligonucleotide functionalized surfaces as a function of salt concentration and temperature. Kinetic and thermodynamic parameters derived from the SPR reflectivity data are used to evaluate the effect of multivalence on the strength of interaction. These results allow us to define thermal processing strategies that will discriminate between partially and fully bound structure-substrate complexes or to reengineer the interactions to facilitate discrimination. Controlling the interactions between self-assembling soft matter with hard matter substrates is an essential step towards future applications of DNA nanostructures as length scale bridging interfaces.