hi, I’m Kim,
for the 1st time I over wintered my roses with burlap…One bush has brown canker at the base and the canes are brown…some with green at the top portion. There is new growth at the base. Do I need to prune the canker with green tops? I have begun spraying to stop the fungus.
Yes, the new growth above the canker will soon die. To prevent the canker from moving down the stem to the base, lethal to the rose, prune off all visible portions and several inches into good-looking cane and pith. You may have already seen this article on brown canker: https://www.gardeningknowhow.com/ornamental/flowers/roses/brown-canker-roses.htm