The nanomachines meme is commonly posted in /h/ or /d/ in threads involving characters from the anime My Otome, using the phrase o noes her nanomachines!!!11. In the show, the super-powered Otome's nanoamachines -- implantations which are the source of their power -- are adversely affected by prostate-specific antigen, due to their bodies to generating antibodies that destroy the nanomachines. For this reason, they must remain virgins until they "retire" from their duties (or, as /a/ssholes point out, be gay).
The exact mechanics of how this happens is glossed over. Further questions raised by fans are why the nanomachines cannot be made resistant to PSA, whether semen entering any mucous membranes is dangerous and precludes sex, whether it's possible to retire an Otome just by spraying her with semen or, most prominently, why they don't just use condoms. Most accept this as a plot device to explain the exclusively female use of them, but also the appeal to the standard otaku's fetish of virginal moeblobs.
In a nutshell, any time hentai of an Otome having sex with a man appears, she's just been retired, thus the alarmed cry of o noes her nanomachines!!11. Additionally, the phrase I'd break her nanomachines (or variations thereof) are used as an Otome-specific alternative to "I'd hit it".