Products, compositions, systems, and methods for modifying a target structurewhich mediates or is associatedwith a biological activity, including treatment of conditions, disorders, ordiseases mediated by or associated with a targetstructure, such as a virus, cell, subcellular structure or extracellularstructure. The methods may be performed in situ in a non-invasivemanner by application of an initiation energy to a subject thus producing aneffect on or change to the target structure directly orvia a modulation agent. The methods may further be performed by application ofan initiation energy to a subject in situ to activatea pharmaceutical agent directly or via an energy modulation agent, optionallyin the presence of one or more plasmonics activeagents, thus producing an effect on or change to the target structure. Kitscontaining products or compositions formulated orconfigured and systems for use in practicing these methods.