Revision history [back]

Mat erase_mask = Mat::zeros(labels.rows, labels.cols, CV_8U);
for(int i = 1; i<num_components; ++i) //Iterate over labels
{
    Mat mask = labels == i; //Keep only the label in question
    int area = findNonZero(mask); //Find the area of the label
    if(area < area_threshold) //Your condition
       bitwise_or(erase_mask, mask, erase_mask); //Save the area to erase
}
labels.setTo(0, erase_mask);  //Actually erase them

Or you can use connectedComponentsWithStats and it will give you an area value. That would be faster, especially if you used the bounding box as an ROI. More complicated though, so I just gave you this.