Philip Treloar, a Eufor spokesman, said: "The aim of the operation is to find material and information that could assist the ICTY (International Criminal Tribunal for the Former Yugoslavia) in the search for persons indicted for war crimes."
He said the raid aimed to put pressure on the networks that support Karadzic in hiding.
The houses have been raided dozens of times since Karadzic went on the run at the end of the Bosnia war.
Treloar said the operation finished around noon local time (1100 GMT) on Thursday and that "items of interest" had been taken away.
Popov, who runs an accounting service, told local media that the troops had taken documents related to her company as well as her telephones and computers.
He said "It is believed that these people are associated with Radovan Karadzic's support network. There are items of interest that have been taken and they will be examined."
The UN war crimes tribunal in The Hague has indicted Karadzic and his military leader Ratko Mladic for genocide over the 1995 Srebrenica massacre of 8,000 Muslims and the 43-month siege of Sarajevo that claimed some 11,000 lives.
The court says Mladic is hiding in Serbia, Karadzic is believed to be moving between eastern Bosnia, Serbia and Montenegro.