Complex nonlinear optical materials comprising elemental, compound or alloy quantum dots embedded in appropriate dielectric or semiconducting hosts may be suitable for deployment in photonic devices. Ion implantation, ion exchange followed by ion implantation, and pulsed laser deposition have all been used to synthesize these materials. However, the correlation between the parameters of energetic-beam synthesis and the nonlinear optical properties is still very rudimentary when one starts to ask what is happening at nanoscale dimensions. Systems integration of corplex nonlinear optical materials requires that the mesoscale materials science be well understood within the context of device structures. We discuss the effects of beam energy and energy density on quantum-dot size and spatial distribution, thermal conductivity, quantum-dot composition, crystallinity and defects — and, in turn, on the third-order optical susceptibility of the composite material. Examples from recent work in our laboratories are used to illustrate these effects.