A nanorobot is not necessarily a very tiny version of a full-sized robot, but it is very tiny. 'Nano-' means 1/1,000,000,000. Just as a millimeter ir 1/1,000,000 of a meter, so a nanometer is 1/1,000,000,000 of a meter. Nanorobots are extremely tiny robots (although not necessarily of the classic human form robot) that could theoretically be used to perform surgery by attacking similar-sized invaders, whether virus, bacterium, or what ever.
In Atom's case, just as in Fry's
(see futurama episode "Parasites Lost"), nanorobots are remote controlled miniature versions of the full-sized items. Thus, the person controls or becomes the miniature version, he sees, hears, and feels everything that the remote-controlled nanorobot does. When he moves his arm, the nanorobot moves its arm.
I will refrain from offering any spoilers here.
Does he use 
