We should probably try to confine the nanorobots so they run out of resources with which to replicate. However we will have to confine them with a substance that they can't use to replicate with -maybe we could surround them with water...or a magnetic field.....or fire...or something. If they don't have resources, the nanorobots won't be able to make copies of themselves anymore. Meanwhile we should actively destroy all the nanorobots that we can because at least the ones we destroy can't replicate anymore. Since the nanorobots' replication is similar to that of bacteria, depriving them of resources would work well since that is how you get bacteria to stop growing (when bacteria are grown in a culture they stop growing when they use up all the resources in the culture).

Self replication produces an exact copy of the organism that is replicating - if adult humans could self-replicate, they would produce exact copies of themselves - the replicas would even be the same age as the original person. Clones, however, are born as babies and have to grow up before they become like the original person. Thus self-replication would be a lot more dangerous because it happens much faster and produces exact copies rather than infants.

sources:

http://www.worldwidewords.org/turnsofphrase/tp-gre3.htm
http://www.kurzweilai.net/meme/frame.html?main=/articles/art0142.html?
http://www.iop.org/EJ/news/-topic%3D763/journal/0957-4484