If there are only a few specific or scattered houses you can drop an invisible box on the right place (the center of your target). This will clear the area from single autogen (not grouped) elements in a radius of ca. 30 meters, if I recall right. Grouped elements, like groves, or rather large objects are a bit more difficult because technically the placement of an element is by referencing their center point, which might be outside the circle of effectiveness of the dummy box. The sim does not know how big the element is, it only goes by the center point. Hence the "spilling" of large autogen objects at some times.
HTH and cheers,
Mark