“Then Judas detailed men to fight against those in the citadel until he had cleansed the sanctuary. He chose blameless priests devoted to the law. They cleansed the sanctuary. They removed the defiled stones to an unclean place.”
Apparently there was still a garrison of Syrian troops in the Jerusalem citadel. Judas sent some troops to keep them occupied while he cleaned up the sanctuary. It is not clear why he did not wipe them out, but they seem to be a persistent problem. Anyway, he chose some blameless priests who were devoted to the law to clean up the sanctuary. They removed all the defiled stones and brought them to some unclean place, probably outside the city.