In order to control nanomachines via external signals, it will be necessary to use multiple actuators that can be activated independently.
Molecular structure is largely determined by where the electrons are. If the electrons can be made to move, the molecule may change shape. For some molecules, hitting them with light can make the electrons move. Thus, light-actuated molecular actuators have already been developed.
It would be nice if, instead of just "light," there was a whole palette of actuators, each activated by a different color. It would be nice if, instead of having to develop each one individually, a general approach could create a whole family of these actuators.
Nanotech solar cell research has explored ways that light energy can be transferred from one molecule to another - connect one molecule that absorbs the photon to another that creates electricity or hydrogen. So what if, instead of building an actuator molecule that both absorbs photons and moves, build one that doesn't absorb any photons - but can accept photon energy from a nanoparticle it's connected to?
It seems like this scheme would allow a variety of actuators to be built, sensitive to different frequencies of light, simply by swapping out the nanoparticles. Frequency-specific nanoparticles already exist, and the frequency can be tuned simply by adjusting the size of the nanoparticle when it's fabricated.
I'm not up to date on the relevant research, so this idea may already have been proposed elsewhere. And, of course, it may not work. But it seems plausible... and if it did work, it would provide a means of broadcast control of nanomachines, without needing physical macro/nano contact, and with multiple actuators individually controllable.